bio-samtools 0.4.1 → 0.4.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/VERSION +1 -1
- data/bio-samtools.gemspec +60 -6
- data/doc/Bio.html +171 -0
- data/doc/Bio/DB.html +163 -0
- data/doc/Bio/DB/Alignment.html +780 -0
- data/doc/Bio/DB/SAM.html +1241 -0
- data/doc/Bio/DB/SAM/Library.html +217 -0
- data/doc/Bio/DB/SAM/Tools.html +331 -0
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
- data/doc/Bio/DB/SAMException.html +205 -0
- data/doc/Bio/DB/Tag.html +254 -0
- data/doc/LICENSE_txt.html +881 -0
- data/doc/LibC.html +153 -0
- data/doc/Pileup.html +571 -0
- data/doc/Vcf.html +473 -0
- data/doc/created.rid +10 -1
- data/doc/images/add.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
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- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
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- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
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- data/doc/images/tag_green.png +0 -0
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- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +109 -21
- data/doc/js/darkfish.js +153 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/lib/bio-samtools_rb.html +115 -0
- data/doc/lib/bio/db/sam/bam_rb.html +121 -0
- data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
- data/doc/lib/bio/db/sam/library_rb.html +115 -0
- data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
- data/doc/lib/bio/db/sam/sam_rb.html +121 -0
- data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
- data/doc/lib/bio/db/sam_rb.html +115 -0
- data/doc/rdoc.css +543 -0
- data/doc/table_of_contents.html +186 -0
- data/ext/Makefile-bioruby.patch +1 -1
- data/ext/Rakefile +8 -1
- data/ext/mkrf_conf.rb +8 -1
- data/lib/bio/db/sam.rb +140 -27
- data/lib/bio/db/sam/vcf.rb +0 -1
- data/test/basictest.rb +4 -4
- data/test/test_basic.rb +50 -34
- metadata +79 -25
- data/test/coverage.rb +0 -26
- data/test/coverage_plot.rb +0 -28
- data/test/feature.rb +0 -0
- data/test/test_pileup.rb +0 -68
data/doc/Bio/DB/SAM.html
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<li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
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<h1 class="class">class Bio::DB::Sam</h1>
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<div id="description" class="description">
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<!-- Attributes -->
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<p>If true, the RG tag is added (infered from the filenames)</p>
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|
+
</dd><dt>by_qname
|
|
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|
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<dd>
|
|
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|
+
<p>If true, the bamfiles should by ordered by query name, if false, by
|
|
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|
+
coordinates.</p>
|
|
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|
+
</dd></dl>
|
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|
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|
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|
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|
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|
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|
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|
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<div class="method-source-code" id="merge-source">
|
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|
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<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 259</span>
|
|
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|
+
<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">files</span>, <span class="ruby-identifier">merged_file</span>, <span class="ruby-identifier">headers</span>, <span class="ruby-identifier">add_RG</span>, <span class="ruby-identifier">by_qname</span>)
|
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|
+
<span class="ruby-identifier">strptrs</span> = []
|
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|
+
<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-string">"merge"</span>)
|
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|
+
<span class="ruby-identifier">files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
|
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|
+
<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">file</span>)
|
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|
+
<span class="ruby-keyword">end</span>
|
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<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-keyword">nil</span>
|
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291
|
+
|
|
292
|
+
<span class="ruby-comment"># Now load all the pointers into a native memory block</span>
|
|
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|
+
<span class="ruby-identifier">argv</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
|
|
294
|
+
<span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
295
|
+
<span class="ruby-identifier">argv</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">put_pointer</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">p</span>)
|
|
296
|
+
<span class="ruby-keyword">end</span>
|
|
297
|
+
<span class="ruby-comment">#void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)</span>
|
|
298
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_merge_core</span>(<span class="ruby-identifier">by_qname</span>, <span class="ruby-identifier">merged_file</span>, <span class="ruby-identifier">headers</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">argv</span>, <span class="ruby-identifier">add_RG</span>)
|
|
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|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
+
</div><!-- merge-source -->
|
|
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|
+
|
|
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|
+
</div>
|
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|
+
|
|
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|
+
|
|
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|
+
|
|
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|
+
|
|
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|
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</div><!-- merge-method -->
|
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|
+
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|
+
|
|
310
|
+
<div id="method-c-new" class="method-detail ">
|
|
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|
+
|
|
312
|
+
<div class="method-heading">
|
|
313
|
+
<span class="method-name">new</span><span
|
|
314
|
+
class="method-args">(optsa={})</span>
|
|
315
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
316
|
+
</div>
|
|
317
|
+
|
|
318
|
+
|
|
319
|
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<div class="method-description">
|
|
320
|
+
|
|
321
|
+
<p>To make a new sam object. Initialize expects a hash optsa with the
|
|
322
|
+
following elemets:</p>
|
|
323
|
+
<dl class="rdoc-list note-list"><dt>fasta
|
|
324
|
+
<dd>
|
|
325
|
+
<p>The fasta file with the reference. (nil)</p>
|
|
326
|
+
</dd><dt>bam
|
|
327
|
+
<dd>
|
|
328
|
+
<p>path to a binary <a href="SAM.html">SAM</a> file (nil)</p>
|
|
329
|
+
</dd><dt>tam
|
|
330
|
+
<dd>
|
|
331
|
+
<p>path to a text <a href="SAM.html">SAM</a> file (nil)</p>
|
|
332
|
+
</dd><dt>compressed
|
|
333
|
+
<dd>
|
|
334
|
+
<p>If the binary file is compressed (true)</p>
|
|
335
|
+
</dd><dt>write
|
|
336
|
+
<dd>
|
|
337
|
+
<p>If the file is to be writen (false). Not supported yet.</p>
|
|
338
|
+
</dd></dl>
|
|
339
|
+
|
|
340
|
+
<p><strong>NOTE:</strong> you can’t use binary and text formats
|
|
341
|
+
simultaneusly. To make queries, the file has to be a sorted binary. This
|
|
342
|
+
function doesn’t actually open the file, it just prepares the object to
|
|
343
|
+
be opened in a later stage.</p>
|
|
344
|
+
|
|
345
|
+
|
|
346
|
+
|
|
347
|
+
<div class="method-source-code" id="new-source">
|
|
348
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 29</span>
|
|
349
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">optsa</span>={})
|
|
350
|
+
<span class="ruby-identifier">opts</span> = { <span class="ruby-value">:fasta</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">nil</span>, <span class="ruby-value">:bam</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">nil</span>,<span class="ruby-value">:tam</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">nil</span>, <span class="ruby-value">:compressed</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">true</span>, <span class="ruby-value">:write</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">false</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">optsa</span>)
|
|
351
|
+
|
|
352
|
+
|
|
353
|
+
|
|
354
|
+
<span class="ruby-ivar">@fasta_path</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:fasta</span>]
|
|
355
|
+
<span class="ruby-ivar">@compressed</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:compressed</span>]
|
|
356
|
+
<span class="ruby-ivar">@write</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:write</span>]
|
|
357
|
+
<span class="ruby-identifier">bam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:bam</span>]
|
|
358
|
+
<span class="ruby-identifier">tam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:tam</span>]
|
|
359
|
+
|
|
360
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">&&</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">&&</span> <span class="ruby-ivar">@fasta_path</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
|
|
361
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No alignment or reference file"</span>
|
|
362
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">&&</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
|
|
363
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Alignment has to be in either text or binary format, not both"</span>
|
|
364
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
|
|
365
|
+
<span class="ruby-ivar">@binary</span> = <span class="ruby-keyword">true</span>
|
|
366
|
+
<span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">bam</span>
|
|
367
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
|
|
368
|
+
<span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">tam</span>
|
|
369
|
+
<span class="ruby-ivar">@binary</span> = <span class="ruby-keyword">false</span>
|
|
370
|
+
|
|
371
|
+
<span class="ruby-keyword">end</span>
|
|
372
|
+
<span class="ruby-ivar">@fasta_file</span> = <span class="ruby-keyword">nil</span>
|
|
373
|
+
<span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword">nil</span>
|
|
374
|
+
|
|
375
|
+
<span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-value">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
|
|
376
|
+
<span class="ruby-keyword">end</span></pre>
|
|
377
|
+
</div><!-- new-source -->
|
|
378
|
+
|
|
379
|
+
</div>
|
|
380
|
+
|
|
381
|
+
|
|
382
|
+
|
|
383
|
+
|
|
384
|
+
</div><!-- new-method -->
|
|
385
|
+
|
|
386
|
+
|
|
387
|
+
</section><!-- public-class-method-details -->
|
|
388
|
+
|
|
389
|
+
<section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
|
|
390
|
+
<h3 class="section-header">Public Instance Methods</h3>
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
<div id="method-i-average_coverage" class="method-detail ">
|
|
394
|
+
|
|
395
|
+
<div class="method-heading">
|
|
396
|
+
<span class="method-name">average_coverage</span><span
|
|
397
|
+
class="method-args">(chromosome, qstart, len)</span>
|
|
398
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
399
|
+
</div>
|
|
400
|
+
|
|
401
|
+
|
|
402
|
+
<div class="method-description">
|
|
403
|
+
|
|
404
|
+
<p>Returns the average coverage of a region in a bam file.</p>
|
|
405
|
+
|
|
406
|
+
|
|
407
|
+
|
|
408
|
+
<div class="method-source-code" id="average_coverage-source">
|
|
409
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 143</span>
|
|
410
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">average_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
|
|
411
|
+
|
|
412
|
+
<span class="ruby-comment">#reference = fetch_reference(chromosome, qstart,len)</span>
|
|
413
|
+
<span class="ruby-comment"># len = reference.length if len > reference.length</span>
|
|
414
|
+
|
|
415
|
+
|
|
416
|
+
<span class="ruby-identifier">coverages</span> = <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
|
|
417
|
+
<span class="ruby-identifier">total</span> = <span class="ruby-value">0</span>
|
|
418
|
+
<span class="ruby-identifier">len</span>.<span class="ruby-identifier">times</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">total</span>= <span class="ruby-identifier">total</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span>] }
|
|
419
|
+
<span class="ruby-identifier">avg_cov</span> = <span class="ruby-identifier">total</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">len</span>
|
|
420
|
+
<span class="ruby-comment">#LibC.free reference</span>
|
|
421
|
+
<span class="ruby-identifier">avg_cov</span>
|
|
422
|
+
<span class="ruby-keyword">end</span></pre>
|
|
423
|
+
</div><!-- average_coverage-source -->
|
|
424
|
+
|
|
425
|
+
</div>
|
|
426
|
+
|
|
427
|
+
|
|
428
|
+
|
|
429
|
+
|
|
430
|
+
</div><!-- average_coverage-method -->
|
|
431
|
+
|
|
432
|
+
|
|
433
|
+
<div id="method-i-chromosome_coverage" class="method-detail ">
|
|
434
|
+
|
|
435
|
+
<div class="method-heading">
|
|
436
|
+
<span class="method-name">chromosome_coverage</span><span
|
|
437
|
+
class="method-args">(chromosome, qstart, len)</span>
|
|
438
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
439
|
+
</div>
|
|
440
|
+
|
|
441
|
+
|
|
442
|
+
<div class="method-description">
|
|
443
|
+
|
|
444
|
+
<p>Returns an array with the coverage at each possition in the queried region
|
|
445
|
+
This is a simple average coverage just calculated with the first and last
|
|
446
|
+
possition of the alignment, ignoring the gaps.</p>
|
|
447
|
+
|
|
448
|
+
|
|
449
|
+
|
|
450
|
+
<div class="method-source-code" id="chromosome_coverage-source">
|
|
451
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 160</span>
|
|
452
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
|
|
453
|
+
<span class="ruby-comment"># reference = fetch_reference(chromosome, qstart,len)</span>
|
|
454
|
+
<span class="ruby-comment"># len = reference.length if len > reference.length</span>
|
|
455
|
+
<span class="ruby-comment">#p qend.to_s + "-" + qstart.to_s + "framesize " + (qend - qstart).to_s</span>
|
|
456
|
+
<span class="ruby-identifier">coverages</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">len</span>, <span class="ruby-value">0</span>)
|
|
457
|
+
|
|
458
|
+
<span class="ruby-identifier">chr_cov_proc</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
|
|
459
|
+
<span class="ruby-comment">#last = qstart + len</span>
|
|
460
|
+
<span class="ruby-comment">#first = qstart</span>
|
|
461
|
+
<span class="ruby-comment">#last = alignment.calend if last > alignment.calend</span>
|
|
462
|
+
<span class="ruby-comment">#first = alignment.pos if first < alignment.pos</span>
|
|
463
|
+
<span class="ruby-comment"># p first</span>
|
|
464
|
+
<span class="ruby-identifier">last</span> = <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">calend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">qstart</span>
|
|
465
|
+
<span class="ruby-identifier">first</span> = <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">qstart</span>
|
|
466
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">last</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">first</span>
|
|
467
|
+
<span class="ruby-identifier">tmp</span> = <span class="ruby-identifier">last</span>
|
|
468
|
+
<span class="ruby-identifier">last</span> = <span class="ruby-identifier">first</span>
|
|
469
|
+
<span class="ruby-identifier">first</span> = <span class="ruby-identifier">last</span>
|
|
470
|
+
<span class="ruby-keyword">end</span>
|
|
471
|
+
|
|
472
|
+
<span class="ruby-comment"># STDERR.puts "#{first} #{last}\n"</span>
|
|
473
|
+
<span class="ruby-identifier">first</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">last</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
474
|
+
|
|
475
|
+
<span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>] = <span class="ruby-value">1</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>] <span class="ruby-keyword">if</span> <span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">len</span> <span class="ruby-operator">&&</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
476
|
+
}
|
|
477
|
+
<span class="ruby-keyword">end</span>
|
|
478
|
+
|
|
479
|
+
<span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qstart</span><span class="ruby-operator">+</span><span class="ruby-identifier">len</span>, <span class="ruby-identifier">chr_cov_proc</span>)
|
|
480
|
+
<span class="ruby-comment">#p coverages</span>
|
|
481
|
+
<span class="ruby-identifier">coverages</span>
|
|
482
|
+
<span class="ruby-keyword">end</span></pre>
|
|
483
|
+
</div><!-- chromosome_coverage-source -->
|
|
484
|
+
|
|
485
|
+
</div>
|
|
486
|
+
|
|
487
|
+
|
|
488
|
+
|
|
489
|
+
|
|
490
|
+
</div><!-- chromosome_coverage-method -->
|
|
491
|
+
|
|
492
|
+
|
|
493
|
+
<div id="method-i-close" class="method-detail ">
|
|
494
|
+
|
|
495
|
+
<div class="method-heading">
|
|
496
|
+
<span class="method-name">close</span><span
|
|
497
|
+
class="method-args">()</span>
|
|
498
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
499
|
+
</div>
|
|
500
|
+
|
|
501
|
+
|
|
502
|
+
<div class="method-description">
|
|
503
|
+
|
|
504
|
+
<p>Closes the sam file and destroys the C pointers using the functions
|
|
505
|
+
provided by libbam</p>
|
|
506
|
+
|
|
507
|
+
|
|
508
|
+
|
|
509
|
+
<div class="method-source-code" id="close-source">
|
|
510
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 95</span>
|
|
511
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">close</span>()
|
|
512
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_destroy</span>(<span class="ruby-ivar">@fasta_index</span>) <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
|
|
513
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_destroy</span>(<span class="ruby-ivar">@sam_index</span>) <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
|
|
514
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">samclose</span>(<span class="ruby-ivar">@sam_file</span>) <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam_file</span>.<span class="ruby-identifier">nil?</span>
|
|
515
|
+
<span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword">nil</span>
|
|
516
|
+
<span class="ruby-ivar">@fasta_index</span> = <span class="ruby-keyword">nil</span>
|
|
517
|
+
<span class="ruby-keyword">end</span></pre>
|
|
518
|
+
</div><!-- close-source -->
|
|
519
|
+
|
|
520
|
+
</div>
|
|
521
|
+
|
|
522
|
+
|
|
523
|
+
|
|
524
|
+
|
|
525
|
+
</div><!-- close-method -->
|
|
526
|
+
|
|
527
|
+
|
|
528
|
+
<div id="method-i-deprecated_pileup" class="method-detail ">
|
|
529
|
+
|
|
530
|
+
<div class="method-heading">
|
|
531
|
+
<span class="method-name">deprecated_pileup</span><span
|
|
532
|
+
class="method-args">( cmd ) { |pileup| ... }</span>
|
|
533
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
534
|
+
</div>
|
|
535
|
+
|
|
536
|
+
|
|
537
|
+
<div class="method-description">
|
|
538
|
+
|
|
539
|
+
<p>utility method that does not use the samtools API, it calls samtools
|
|
540
|
+
directly as if on the command line and catches the output, to use this
|
|
541
|
+
method you must have a version of samtools that supports the pileup command
|
|
542
|
+
(< 0.1.17) otherwise the command will fail. mpileup is the preferred
|
|
543
|
+
method for getting pileups. With this method the sam object should be
|
|
544
|
+
created as usual, but you need to pass this method a string of options for
|
|
545
|
+
samtools you don’t need to provide the call to samtools pileup itself or
|
|
546
|
+
-f <fasta file> or the bam file itself, these are taken from the sam
|
|
547
|
+
object</p>
|
|
548
|
+
|
|
549
|
+
|
|
550
|
+
|
|
551
|
+
<div class="method-source-code" id="deprecated_pileup-source">
|
|
552
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 472</span>
|
|
553
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">deprecated_pileup</span>( <span class="ruby-identifier">cmd</span> )
|
|
554
|
+
|
|
555
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-string">'samtools pileup > /dev/null 2>&1'</span>)
|
|
556
|
+
<span class="ruby-comment">##assumes samtools is in the path...</span>
|
|
557
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">$?</span>.<span class="ruby-identifier">exitstatus</span> <span class="ruby-operator">></span> <span class="ruby-value">1</span>
|
|
558
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">RuntimeError</span>, <span class="ruby-string">"samtools is required on the path. A version of samtools with the pileup function is required"</span>
|
|
559
|
+
<span class="ruby-keyword">end</span>
|
|
560
|
+
|
|
561
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No BAMFile provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
|
|
562
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No FastA provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
|
|
563
|
+
|
|
564
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-string">'samtools pileup '</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">cmd</span> <span class="ruby-operator">+</span> <span class="ruby-node">" -f #{@fasta_path}"</span> <span class="ruby-operator">+</span> <span class="ruby-node">" #{@sam}"</span>
|
|
565
|
+
|
|
566
|
+
<span class="ruby-identifier">pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">command</span>)
|
|
567
|
+
<span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
|
|
568
|
+
<span class="ruby-keyword">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
569
|
+
<span class="ruby-keyword">end</span>
|
|
570
|
+
<span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">close</span>
|
|
571
|
+
<span class="ruby-keyword">end</span></pre>
|
|
572
|
+
</div><!-- deprecated_pileup-source -->
|
|
573
|
+
|
|
574
|
+
</div>
|
|
575
|
+
|
|
576
|
+
|
|
577
|
+
|
|
578
|
+
|
|
579
|
+
</div><!-- deprecated_pileup-method -->
|
|
580
|
+
|
|
581
|
+
|
|
582
|
+
<div id="method-i-fetch" class="method-detail ">
|
|
583
|
+
|
|
584
|
+
<div class="method-heading">
|
|
585
|
+
<span class="method-name">fetch</span><span
|
|
586
|
+
class="method-args">(chromosome, qstart, qend)</span>
|
|
587
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
588
|
+
</div>
|
|
589
|
+
|
|
590
|
+
|
|
591
|
+
<div class="method-description">
|
|
592
|
+
|
|
593
|
+
<p>Returns an array of Alignments on a given region.</p>
|
|
594
|
+
|
|
595
|
+
|
|
596
|
+
|
|
597
|
+
<div class="method-source-code" id="fetch-source">
|
|
598
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 211</span>
|
|
599
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>)
|
|
600
|
+
<span class="ruby-identifier">als</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
601
|
+
<span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
|
|
602
|
+
<span class="ruby-identifier">als</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">clone</span>)
|
|
603
|
+
<span class="ruby-value">0</span>
|
|
604
|
+
<span class="ruby-keyword">end</span>
|
|
605
|
+
<span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>, <span class="ruby-identifier">fetchAlignment</span>)
|
|
606
|
+
<span class="ruby-identifier">als</span>
|
|
607
|
+
<span class="ruby-keyword">end</span></pre>
|
|
608
|
+
</div><!-- fetch-source -->
|
|
609
|
+
|
|
610
|
+
</div>
|
|
611
|
+
|
|
612
|
+
|
|
613
|
+
|
|
614
|
+
|
|
615
|
+
</div><!-- fetch-method -->
|
|
616
|
+
|
|
617
|
+
|
|
618
|
+
<div id="method-i-fetch_reference" class="method-detail ">
|
|
619
|
+
|
|
620
|
+
<div class="method-heading">
|
|
621
|
+
<span class="method-name">fetch_reference</span><span
|
|
622
|
+
class="method-args">(chromosome, qstart,qend)</span>
|
|
623
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
624
|
+
</div>
|
|
625
|
+
|
|
626
|
+
|
|
627
|
+
<div class="method-description">
|
|
628
|
+
|
|
629
|
+
<p>Returns the sequence for a given region.</p>
|
|
630
|
+
|
|
631
|
+
|
|
632
|
+
|
|
633
|
+
<div class="method-source-code" id="fetch_reference-source">
|
|
634
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 193</span>
|
|
635
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch_reference</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
|
|
636
|
+
<span class="ruby-identifier">load_reference</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
|
|
637
|
+
<span class="ruby-identifier">query</span> = <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
|
|
638
|
+
<span class="ruby-identifier">len</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
|
|
639
|
+
<span class="ruby-identifier">reference</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_fetch</span>(<span class="ruby-ivar">@fasta_index</span>, <span class="ruby-identifier">query</span>, <span class="ruby-identifier">len</span>)
|
|
640
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Unable to get sequence for reference: "</span><span class="ruby-operator">+</span><span class="ruby-identifier">query</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">reference</span>.<span class="ruby-identifier">nil?</span>
|
|
641
|
+
|
|
642
|
+
<span class="ruby-identifier">reference</span>
|
|
643
|
+
<span class="ruby-keyword">end</span></pre>
|
|
644
|
+
</div><!-- fetch_reference-source -->
|
|
645
|
+
|
|
646
|
+
</div>
|
|
647
|
+
|
|
648
|
+
|
|
649
|
+
|
|
650
|
+
|
|
651
|
+
</div><!-- fetch_reference-method -->
|
|
652
|
+
|
|
653
|
+
|
|
654
|
+
<div id="method-i-fetch_with_function" class="method-detail ">
|
|
655
|
+
|
|
656
|
+
<div class="method-heading">
|
|
657
|
+
<span class="method-name">fetch_with_function</span><span
|
|
658
|
+
class="method-args">(chromosome, qstart, qend, function)</span>
|
|
659
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
660
|
+
</div>
|
|
661
|
+
|
|
662
|
+
|
|
663
|
+
<div class="method-description">
|
|
664
|
+
|
|
665
|
+
<p>Executes a function on each <a href="Alignment.html">Alignment</a> inside
|
|
666
|
+
the queried region of the chromosome. The chromosome can be either the
|
|
667
|
+
textual name or a FixNum with the internal index. However, you need to get
|
|
668
|
+
the internal index with the provided API, otherwise the pointer is outside
|
|
669
|
+
the scope of the C library. Returns the count of alignments in the region.
|
|
670
|
+
WARNING: Accepts an index already parsed by the library. It fails when you
|
|
671
|
+
use your own FixNum (FFI-bug?)</p>
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
|
|
675
|
+
<div class="method-source-code" id="fetch_with_function-source">
|
|
676
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 226</span>
|
|
677
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>, <span class="ruby-identifier">function</span>)
|
|
678
|
+
<span class="ruby-identifier">load_index</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
|
|
679
|
+
<span class="ruby-identifier">chr</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
|
|
680
|
+
<span class="ruby-identifier">beg</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
|
|
681
|
+
<span class="ruby-identifier">last</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
|
|
682
|
+
<span class="ruby-identifier">query</span> = <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
|
|
683
|
+
<span class="ruby-identifier">qpointer</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">query</span>)
|
|
684
|
+
<span class="ruby-identifier">header</span> = <span class="ruby-ivar">@sam_file</span>[<span class="ruby-value">:header</span>]
|
|
685
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_parse_region</span>(<span class="ruby-identifier">header</span>,<span class="ruby-identifier">qpointer</span>, <span class="ruby-identifier">chr</span>, <span class="ruby-identifier">beg</span>, <span class="ruby-identifier">last</span>)
|
|
686
|
+
<span class="ruby-comment">#raise SAMException.new(), "invalid query: " + query if(chr.read_int < 0)</span>
|
|
687
|
+
<span class="ruby-identifier">count</span> = <span class="ruby-value">0</span>;
|
|
688
|
+
|
|
689
|
+
<span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">data</span><span class="ruby-operator">|</span>
|
|
690
|
+
<span class="ruby-identifier">alignment</span> = <span class="ruby-constant">Alignment</span>.<span class="ruby-identifier">new</span>
|
|
691
|
+
<span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">header</span>)
|
|
692
|
+
<span class="ruby-identifier">function</span>.<span class="ruby-identifier">call</span>(<span class="ruby-identifier">alignment</span>)
|
|
693
|
+
<span class="ruby-identifier">count</span> = <span class="ruby-identifier">count</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
|
|
694
|
+
<span class="ruby-value">0</span>
|
|
695
|
+
<span class="ruby-keyword">end</span>
|
|
696
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_fetch</span>(<span class="ruby-ivar">@sam_file</span>[<span class="ruby-value">:x</span>][<span class="ruby-value">:bam</span>], <span class="ruby-ivar">@sam_index</span>,<span class="ruby-identifier">chr</span>.<span class="ruby-identifier">read_int</span>,<span class="ruby-identifier">beg</span>.<span class="ruby-identifier">read_int</span>, <span class="ruby-identifier">last</span>.<span class="ruby-identifier">read_int</span>, <span class="ruby-keyword">nil</span>, <span class="ruby-identifier">fetchAlignment</span>)
|
|
697
|
+
<span class="ruby-comment">#LibC.free chr</span>
|
|
698
|
+
<span class="ruby-comment">#LibC.free beg</span>
|
|
699
|
+
<span class="ruby-comment">#LibC.free last</span>
|
|
700
|
+
<span class="ruby-comment">#LibC.free qpointer</span>
|
|
701
|
+
<span class="ruby-identifier">count</span>
|
|
702
|
+
<span class="ruby-keyword">end</span></pre>
|
|
703
|
+
</div><!-- fetch_with_function-source -->
|
|
704
|
+
|
|
705
|
+
</div>
|
|
706
|
+
|
|
707
|
+
|
|
708
|
+
|
|
709
|
+
|
|
710
|
+
</div><!-- fetch_with_function-method -->
|
|
711
|
+
|
|
712
|
+
|
|
713
|
+
<div id="method-i-index_stats" class="method-detail ">
|
|
714
|
+
|
|
715
|
+
<div class="method-heading">
|
|
716
|
+
<span class="method-name">index_stats</span><span
|
|
717
|
+
class="method-args">()</span>
|
|
718
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
719
|
+
</div>
|
|
720
|
+
|
|
721
|
+
|
|
722
|
+
<div class="method-description">
|
|
723
|
+
|
|
724
|
+
|
|
725
|
+
|
|
726
|
+
|
|
727
|
+
|
|
728
|
+
<div class="method-source-code" id="index_stats-source">
|
|
729
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 493</span>
|
|
730
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">index_stats</span>
|
|
731
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No BAMFile provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
|
|
732
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No FastA provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
|
|
733
|
+
<span class="ruby-identifier">strptrs</span> = []
|
|
734
|
+
<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-string">"idxstats"</span>)
|
|
735
|
+
<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-ivar">@sam</span>)
|
|
736
|
+
<span class="ruby-identifier">strptrs</span> <span class="ruby-operator"><<</span> <span class="ruby-keyword">nil</span>
|
|
737
|
+
|
|
738
|
+
<span class="ruby-comment"># Now load all the pointers into a native memory block</span>
|
|
739
|
+
<span class="ruby-identifier">argv</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
|
|
740
|
+
<span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
741
|
+
<span class="ruby-identifier">argv</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">put_pointer</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">p</span>)
|
|
742
|
+
<span class="ruby-keyword">end</span>
|
|
743
|
+
|
|
744
|
+
<span class="ruby-identifier">index_stats</span> = {}
|
|
745
|
+
|
|
746
|
+
<span class="ruby-identifier">old_stdout</span> = <span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">clone</span>
|
|
747
|
+
<span class="ruby-identifier">read_pipe</span>, <span class="ruby-identifier">write_pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">pipe</span>()
|
|
748
|
+
<span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">reopen</span>(<span class="ruby-identifier">write_pipe</span>)
|
|
749
|
+
|
|
750
|
+
<span class="ruby-comment">#int bam_idxstats(int argc, char *argv[])</span>
|
|
751
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_idxstats</span>(<span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>,<span class="ruby-identifier">argv</span>)
|
|
752
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">fork</span>
|
|
753
|
+
<span class="ruby-identifier">write_pipe</span>.<span class="ruby-identifier">close</span>
|
|
754
|
+
<span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">reopen</span>(<span class="ruby-identifier">old_stdout</span>) <span class="ruby-comment">#beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
|
|
755
|
+
<span class="ruby-keyword">begin</span>
|
|
756
|
+
|
|
757
|
+
<span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">readline</span> <span class="ruby-comment">#TAB delimited with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads.</span>
|
|
758
|
+
<span class="ruby-identifier">info</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
|
|
759
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">info</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">4</span>
|
|
760
|
+
<span class="ruby-identifier">index_stats</span>[ <span class="ruby-identifier">info</span>[<span class="ruby-value">0</span>] ] = {<span class="ruby-value">:length</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">info</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:mapped_reads</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">info</span>[<span class="ruby-value">2</span>].<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:unmapped_reads</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">info</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span> }
|
|
761
|
+
<span class="ruby-keyword">end</span>
|
|
762
|
+
<span class="ruby-keyword">rescue</span> <span class="ruby-constant">EOFError</span>
|
|
763
|
+
<span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">close</span>
|
|
764
|
+
<span class="ruby-constant">Process</span>.<span class="ruby-identifier">wait</span>
|
|
765
|
+
<span class="ruby-keyword">end</span>
|
|
766
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#fork</span>
|
|
767
|
+
<span class="ruby-identifier">index_stats</span>
|
|
768
|
+
<span class="ruby-keyword">end</span></pre>
|
|
769
|
+
</div><!-- index_stats-source -->
|
|
770
|
+
|
|
771
|
+
</div>
|
|
772
|
+
|
|
773
|
+
|
|
774
|
+
|
|
775
|
+
|
|
776
|
+
</div><!-- index_stats-method -->
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
<div id="method-i-load_index" class="method-detail ">
|
|
780
|
+
|
|
781
|
+
<div class="method-heading">
|
|
782
|
+
<span class="method-name">load_index</span><span
|
|
783
|
+
class="method-args">()</span>
|
|
784
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
785
|
+
</div>
|
|
786
|
+
|
|
787
|
+
|
|
788
|
+
<div class="method-description">
|
|
789
|
+
|
|
790
|
+
<p>Loads the bam index to be used for fetching. If the index doesn’t exists
|
|
791
|
+
the index is built provided that the user has writing access to the folder
|
|
792
|
+
where the BAM file is located. If the creation of the file fails a <a
|
|
793
|
+
href="SAMException.html">SAMException</a> is thrown. If the index
|
|
794
|
+
doesn’t exist, loading it will take more time. It is suggested to
|
|
795
|
+
generate the index separatedly if the bam file sits on a server where the
|
|
796
|
+
executing user may not have writing permissions in the server.</p>
|
|
797
|
+
|
|
798
|
+
|
|
799
|
+
|
|
800
|
+
<div class="method-source-code" id="load_index-source">
|
|
801
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 114</span>
|
|
802
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">load_index</span>()
|
|
803
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Indexes are only supported by BAM files, please use samtools to convert your SAM file"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@binary</span>
|
|
804
|
+
<span class="ruby-ivar">@sam_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_load</span>(<span class="ruby-ivar">@sam</span>)
|
|
805
|
+
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword">then</span>
|
|
806
|
+
<span class="ruby-identifier">p</span> <span class="ruby-string">"Generating index for: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
|
|
807
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_build</span>(<span class="ruby-ivar">@sam</span>)
|
|
808
|
+
<span class="ruby-ivar">@sam_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_load</span>(<span class="ruby-ivar">@sam</span>)
|
|
809
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Unable to generate bam index for: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
|
|
810
|
+
<span class="ruby-keyword">end</span>
|
|
811
|
+
<span class="ruby-keyword">end</span></pre>
|
|
812
|
+
</div><!-- load_index-source -->
|
|
813
|
+
|
|
814
|
+
</div>
|
|
815
|
+
|
|
816
|
+
|
|
817
|
+
|
|
818
|
+
|
|
819
|
+
</div><!-- load_index-method -->
|
|
820
|
+
|
|
821
|
+
|
|
822
|
+
<div id="method-i-load_reference" class="method-detail ">
|
|
823
|
+
|
|
824
|
+
<div class="method-heading">
|
|
825
|
+
<span class="method-name">load_reference</span><span
|
|
826
|
+
class="method-args">()</span>
|
|
827
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
828
|
+
</div>
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
<div class="method-description">
|
|
832
|
+
|
|
833
|
+
<p>Loads the reference file to be able to query regions of it. This requires
|
|
834
|
+
the fai index to exist in the same folder than the reference. If it
|
|
835
|
+
doesn’t exisits, this functions attempts to generate it. If user
|
|
836
|
+
doesn’t have writing permissions on the folder, or the creation of the
|
|
837
|
+
fai fails for any reason, a <a href="SAMException.html">SAMException</a> is
|
|
838
|
+
thrown.</p>
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
|
|
842
|
+
<div class="method-source-code" id="load_reference-source">
|
|
843
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 128</span>
|
|
844
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">load_reference</span>()
|
|
845
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No path for the refernce fasta file. "</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_path</span>.<span class="ruby-identifier">nil?</span>
|
|
846
|
+
|
|
847
|
+
<span class="ruby-ivar">@fasta_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_load</span>(<span class="ruby-ivar">@fasta_path</span>)
|
|
848
|
+
|
|
849
|
+
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword">then</span>
|
|
850
|
+
<span class="ruby-identifier">p</span> <span class="ruby-string">"Generating index for: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
|
|
851
|
+
<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_build</span>(<span class="ruby-ivar">@fasta_path</span>)
|
|
852
|
+
<span class="ruby-ivar">@fasta_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_load</span>(<span class="ruby-ivar">@fasta_path</span>)
|
|
853
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Unable to generate fasta index for: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
|
|
854
|
+
<span class="ruby-keyword">end</span>
|
|
855
|
+
|
|
856
|
+
<span class="ruby-keyword">end</span></pre>
|
|
857
|
+
</div><!-- load_reference-source -->
|
|
858
|
+
|
|
859
|
+
</div>
|
|
860
|
+
|
|
861
|
+
|
|
862
|
+
|
|
863
|
+
|
|
864
|
+
</div><!-- load_reference-method -->
|
|
865
|
+
|
|
866
|
+
|
|
867
|
+
<div id="method-i-mpileup" class="method-detail ">
|
|
868
|
+
|
|
869
|
+
<div class="method-heading">
|
|
870
|
+
<span class="method-name">mpileup</span><span
|
|
871
|
+
class="method-args">( opts ) { |pileup| ... }</span>
|
|
872
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
873
|
+
</div>
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<div class="method-description">
|
|
877
|
+
|
|
878
|
+
<p>calls the mpileup function, opts is a hash of options identical to the
|
|
879
|
+
command line options for mpileup. is an iterator that yields a <a
|
|
880
|
+
href="../../Pileup.html">Pileup</a> object for each postion the command
|
|
881
|
+
line options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p)
|
|
882
|
+
call the option as a symbol of the flag, eg -r for region is called :r
|
|
883
|
+
=> “some <a href="SAM.html">SAM</a> compatible region” eg
|
|
884
|
+
bam.mpileup(:r => “chr1:1000-2000”, :q => 50) gets the bases with
|
|
885
|
+
quality > 50 on chr1 between 1000-5000</p>
|
|
886
|
+
|
|
887
|
+
|
|
888
|
+
|
|
889
|
+
<div class="method-source-code" id="mpileup-source">
|
|
890
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 281</span>
|
|
891
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup</span>( <span class="ruby-identifier">opts</span> )
|
|
892
|
+
|
|
893
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No BAMFile provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
|
|
894
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No FastA provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
|
|
895
|
+
<span class="ruby-comment">#long option form to short samtools form..</span>
|
|
896
|
+
<span class="ruby-identifier">long_opts</span> = {
|
|
897
|
+
<span class="ruby-value">:region</span> =<span class="ruby-operator">></span> <span class="ruby-value">:r</span>,
|
|
898
|
+
<span class="ruby-value">:illumina_quals</span> =<span class="ruby-operator">></span> <span class="ruby-value">:six</span>,
|
|
899
|
+
<span class="ruby-value">:count_anomalous</span> =<span class="ruby-operator">></span> <span class="ruby-value">:A</span>,
|
|
900
|
+
<span class="ruby-value">:no_baq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:B</span>,
|
|
901
|
+
<span class="ruby-value">:adjust_mapq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:C</span>,
|
|
902
|
+
<span class="ruby-value">:max_per_bam_depth</span> =<span class="ruby-operator">></span> <span class="ruby-value">:d</span>,
|
|
903
|
+
<span class="ruby-value">:extended_baq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:E</span>,
|
|
904
|
+
<span class="ruby-value">:exclude_reads_file</span> =<span class="ruby-operator">></span> <span class="ruby-value">:G</span>,
|
|
905
|
+
<span class="ruby-value">:list_of_positions</span> =<span class="ruby-operator">></span> <span class="ruby-value">:l</span>,
|
|
906
|
+
<span class="ruby-value">:mapping_quality_cap</span> =<span class="ruby-operator">></span> <span class="ruby-value">:M</span>,
|
|
907
|
+
<span class="ruby-value">:ignore_rg</span> =<span class="ruby-operator">></span> <span class="ruby-value">:R</span>,
|
|
908
|
+
<span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">></span> <span class="ruby-value">:q</span>,
|
|
909
|
+
<span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">></span> <span class="ruby-value">:Q</span>
|
|
910
|
+
}
|
|
911
|
+
|
|
912
|
+
<span class="ruby-comment">##convert any long_opts to short opts </span>
|
|
913
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
|
|
914
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
|
|
915
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]] = <span class="ruby-identifier">v</span>
|
|
916
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
|
|
917
|
+
<span class="ruby-keyword">end</span>
|
|
918
|
+
<span class="ruby-keyword">end</span>
|
|
919
|
+
|
|
920
|
+
<span class="ruby-comment">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
|
|
921
|
+
<span class="ruby-comment">##and also associated output options</span>
|
|
922
|
+
[<span class="ruby-value">:g</span>, <span class="ruby-value">:u</span>, <span class="ruby-value">:e</span>, <span class="ruby-value">:h</span>, <span class="ruby-value">:I</span>, <span class="ruby-value">:L</span>, <span class="ruby-value">:o</span>, <span class="ruby-value">:p</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">x</span>) }
|
|
923
|
+
|
|
924
|
+
<span class="ruby-identifier">sam_opts</span> = []
|
|
925
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string("mpileup")</span>
|
|
926
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
|
|
927
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">k</span>] <span class="ruby-comment">##dont bother unless the values provided are true.. </span>
|
|
928
|
+
<span class="ruby-identifier">k</span> = <span class="ruby-string">'6'</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">k</span> <span class="ruby-operator">==</span> <span class="ruby-value">:six</span>
|
|
929
|
+
<span class="ruby-identifier">k</span> = <span class="ruby-string">'-'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span>
|
|
930
|
+
<span class="ruby-identifier">sam_opts</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">k</span> <span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string(k)</span>
|
|
931
|
+
<span class="ruby-identifier">sam_opts</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-keyword">unless</span> [<span class="ruby-string">"-R"</span>, <span class="ruby-string">"-B"</span>, <span class="ruby-string">"-E"</span>, <span class="ruby-string">"-6"</span>, <span class="ruby-string">"-A"</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">k</span>) <span class="ruby-comment">#these are just flags so don't pass a value... strptrs << FFI::MemoryPointer.from_string(v.to_s)</span>
|
|
932
|
+
<span class="ruby-keyword">end</span>
|
|
933
|
+
<span class="ruby-identifier">sam_opts</span> = <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">+</span> [<span class="ruby-string">'-f'</span>, <span class="ruby-ivar">@fasta_path</span>, <span class="ruby-ivar">@sam</span>]
|
|
934
|
+
<span class="ruby-identifier">sam_command</span> = <span class="ruby-node">"#{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')} mpileup #{sam_opts.join(' ')} 2> /dev/null"</span>
|
|
935
|
+
|
|
936
|
+
<span class="ruby-identifier">sam_pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">sam_command</span>)
|
|
937
|
+
<span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">sam_pipe</span>.<span class="ruby-identifier">gets</span>
|
|
938
|
+
<span class="ruby-keyword">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
939
|
+
<span class="ruby-keyword">end</span>
|
|
940
|
+
<span class="ruby-identifier">sam_pipe</span>.<span class="ruby-identifier">close</span>
|
|
941
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string('-f')</span>
|
|
942
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string(@fasta_path)</span>
|
|
943
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string(@sam)</span>
|
|
944
|
+
<span class="ruby-comment">#strptrs << nil</span>
|
|
945
|
+
|
|
946
|
+
<span class="ruby-comment"># Now load all the pointers into a native memory block</span>
|
|
947
|
+
<span class="ruby-comment">#argv = FFI::MemoryPointer.new(:pointer, strptrs.length)</span>
|
|
948
|
+
<span class="ruby-comment">#strptrs.each_with_index do |p, i|</span>
|
|
949
|
+
<span class="ruby-comment"># argv[i].put_pointer(0, p)</span>
|
|
950
|
+
<span class="ruby-comment">#end</span>
|
|
951
|
+
|
|
952
|
+
<span class="ruby-comment">#old_stdout = STDOUT.clone</span>
|
|
953
|
+
<span class="ruby-comment">#read_pipe, write_pipe = IO.pipe()</span>
|
|
954
|
+
<span class="ruby-comment">#STDOUT.reopen(write_pipe)</span>
|
|
955
|
+
<span class="ruby-comment">#int bam_mpileup(int argc, char *argv[])</span>
|
|
956
|
+
<span class="ruby-comment"># Bio::DB::SAM::Tools.bam_mpileup(strptrs.length - 1,argv)</span>
|
|
957
|
+
<span class="ruby-comment">#if fork</span>
|
|
958
|
+
<span class="ruby-comment"># write_pipe.close</span>
|
|
959
|
+
<span class="ruby-comment"># STDOUT.reopen(old_stdout) #beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
|
|
960
|
+
<span class="ruby-comment"># begin</span>
|
|
961
|
+
<span class="ruby-comment"># while line = read_pipe.readline</span>
|
|
962
|
+
<span class="ruby-comment"># yield Pileup.new(line)</span>
|
|
963
|
+
<span class="ruby-comment"># end</span>
|
|
964
|
+
<span class="ruby-comment"># rescue EOFError</span>
|
|
965
|
+
<span class="ruby-comment"># read_pipe.close</span>
|
|
966
|
+
<span class="ruby-comment"># Process.wait</span>
|
|
967
|
+
<span class="ruby-comment"># end</span>
|
|
968
|
+
<span class="ruby-comment">#end</span>
|
|
969
|
+
<span class="ruby-keyword">end</span></pre>
|
|
970
|
+
</div><!-- mpileup-source -->
|
|
971
|
+
|
|
972
|
+
</div>
|
|
973
|
+
|
|
974
|
+
|
|
975
|
+
|
|
976
|
+
|
|
977
|
+
</div><!-- mpileup-method -->
|
|
978
|
+
|
|
979
|
+
|
|
980
|
+
<div id="method-i-mpileup_plus" class="method-detail ">
|
|
981
|
+
|
|
982
|
+
<div class="method-heading">
|
|
983
|
+
<span class="method-name">mpileup_plus</span><span
|
|
984
|
+
class="method-args">( opts ) { |vcf| ... }</span>
|
|
985
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
986
|
+
</div>
|
|
987
|
+
|
|
988
|
+
|
|
989
|
+
<div class="method-description">
|
|
990
|
+
|
|
991
|
+
<p>experimental method that spawns a samtools mpileup | bcftools view process
|
|
992
|
+
and supports returning of pileup vcf</p>
|
|
993
|
+
|
|
994
|
+
<pre>otherwise works like mpileup</pre>
|
|
995
|
+
|
|
996
|
+
|
|
997
|
+
|
|
998
|
+
<div class="method-source-code" id="mpileup_plus-source">
|
|
999
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 363</span>
|
|
1000
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup_plus</span>( <span class="ruby-identifier">opts</span> )
|
|
1001
|
+
|
|
1002
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No BAMFile provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
|
|
1003
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No FastA provided"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
|
|
1004
|
+
<span class="ruby-comment">#long option form to short samtools form..</span>
|
|
1005
|
+
<span class="ruby-identifier">long_opts</span> = {
|
|
1006
|
+
<span class="ruby-value">:region</span> =<span class="ruby-operator">></span> <span class="ruby-value">:r</span>,
|
|
1007
|
+
<span class="ruby-value">:illumina_quals</span> =<span class="ruby-operator">></span> <span class="ruby-value">:six</span>,
|
|
1008
|
+
<span class="ruby-value">:count_anomalous</span> =<span class="ruby-operator">></span> <span class="ruby-value">:A</span>,
|
|
1009
|
+
<span class="ruby-value">:no_baq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:B</span>,
|
|
1010
|
+
<span class="ruby-value">:adjust_mapq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:C</span>,
|
|
1011
|
+
<span class="ruby-value">:max_per_bam_depth</span> =<span class="ruby-operator">></span> <span class="ruby-value">:d</span>,
|
|
1012
|
+
<span class="ruby-value">:extended_baq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:E</span>,
|
|
1013
|
+
<span class="ruby-value">:exclude_reads_file</span> =<span class="ruby-operator">></span> <span class="ruby-value">:G</span>,
|
|
1014
|
+
<span class="ruby-value">:list_of_positions</span> =<span class="ruby-operator">></span> <span class="ruby-value">:l</span>,
|
|
1015
|
+
<span class="ruby-value">:mapping_quality_cap</span> =<span class="ruby-operator">></span> <span class="ruby-value">:M</span>,
|
|
1016
|
+
<span class="ruby-value">:ignore_rg</span> =<span class="ruby-operator">></span> <span class="ruby-value">:R</span>,
|
|
1017
|
+
<span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">></span> <span class="ruby-value">:q</span>,
|
|
1018
|
+
<span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">></span> <span class="ruby-value">:Q</span>,
|
|
1019
|
+
<span class="ruby-comment">###following options are for the -g -u option</span>
|
|
1020
|
+
<span class="ruby-value">:genotype_calling</span> =<span class="ruby-operator">></span> <span class="ruby-value">:g</span>,
|
|
1021
|
+
<span class="ruby-value">:uncompressed_bcf</span> =<span class="ruby-operator">></span> <span class="ruby-value">:u</span>,
|
|
1022
|
+
<span class="ruby-value">:extension_sequencing_probability</span> =<span class="ruby-operator">></span> <span class="ruby-value">:e</span>,
|
|
1023
|
+
<span class="ruby-value">:homopolymer_error_coefficient</span> =<span class="ruby-operator">></span> <span class="ruby-value">:h</span>,
|
|
1024
|
+
<span class="ruby-value">:no_indels</span> =<span class="ruby-operator">></span> <span class="ruby-value">:I</span>,
|
|
1025
|
+
<span class="ruby-value">:skip_indel_over_average_depth</span> =<span class="ruby-operator">></span> <span class="ruby-value">:L</span>,
|
|
1026
|
+
<span class="ruby-value">:gap_open_sequencing_error_probability</span> =<span class="ruby-operator">></span> <span class="ruby-value">:o</span>,
|
|
1027
|
+
<span class="ruby-value">:platforms</span> =<span class="ruby-operator">></span> <span class="ruby-value">:P</span>
|
|
1028
|
+
}
|
|
1029
|
+
|
|
1030
|
+
<span class="ruby-comment">##convert any long_opts to short opts </span>
|
|
1031
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
|
|
1032
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
|
|
1033
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]] = <span class="ruby-identifier">v</span>
|
|
1034
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
|
|
1035
|
+
<span class="ruby-keyword">end</span>
|
|
1036
|
+
<span class="ruby-keyword">end</span>
|
|
1037
|
+
|
|
1038
|
+
<span class="ruby-comment">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
|
|
1039
|
+
<span class="ruby-comment">##and also associated output options</span>
|
|
1040
|
+
<span class="ruby-comment">#[:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }</span>
|
|
1041
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>] = <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:g</span>] <span class="ruby-comment">#so that we always get uncompressed output</span>
|
|
1042
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:g</span>)
|
|
1043
|
+
|
|
1044
|
+
<span class="ruby-identifier">sam_opts</span> = []
|
|
1045
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string("mpileup")</span>
|
|
1046
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
|
|
1047
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">k</span>] <span class="ruby-comment">##dont bother unless the values provided are true.. </span>
|
|
1048
|
+
<span class="ruby-identifier">k</span> = <span class="ruby-string">'6'</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">k</span> <span class="ruby-operator">==</span> <span class="ruby-value">:six</span>
|
|
1049
|
+
<span class="ruby-identifier">k</span> = <span class="ruby-string">'-'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span>
|
|
1050
|
+
<span class="ruby-identifier">sam_opts</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">k</span> <span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string(k)</span>
|
|
1051
|
+
<span class="ruby-identifier">sam_opts</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-keyword">unless</span> [<span class="ruby-string">"-R"</span>, <span class="ruby-string">"-B"</span>, <span class="ruby-string">"-E"</span>, <span class="ruby-string">"-6"</span>, <span class="ruby-string">"-A"</span>, <span class="ruby-string">"-g"</span>, <span class="ruby-string">"-u"</span>, <span class="ruby-string">"-I"</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">k</span>) <span class="ruby-comment">#these are just flags so don't pass a value... strptrs << FFI::MemoryPointer.from_string(v.to_s)</span>
|
|
1052
|
+
<span class="ruby-keyword">end</span>
|
|
1053
|
+
<span class="ruby-identifier">sam_opts</span> = <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">+</span> [<span class="ruby-string">'-f'</span>, <span class="ruby-ivar">@fasta_path</span>, <span class="ruby-ivar">@sam</span>]
|
|
1054
|
+
|
|
1055
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')} mpileup #{sam_opts.join(' ')} 2> /dev/null"</span>
|
|
1056
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>]
|
|
1057
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">command</span> <span class="ruby-operator">+</span> <span class="ruby-node">" | #{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','bcftools')} view -cg -"</span>
|
|
1058
|
+
<span class="ruby-keyword">end</span>
|
|
1059
|
+
<span class="ruby-identifier">pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">command</span>)
|
|
1060
|
+
<span class="ruby-identifier">$stderr</span>.<span class="ruby-identifier">puts</span> <span class="ruby-identifier">command</span>
|
|
1061
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>]
|
|
1062
|
+
<span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
|
|
1063
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'#'</span> <span class="ruby-comment">#skip any header or meta-lines, we dont do anything with those </span>
|
|
1064
|
+
<span class="ruby-keyword">yield</span> <span class="ruby-constant">Vcf</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
1065
|
+
<span class="ruby-keyword">end</span>
|
|
1066
|
+
<span class="ruby-keyword">else</span>
|
|
1067
|
+
<span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
|
|
1068
|
+
<span class="ruby-keyword">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
1069
|
+
<span class="ruby-keyword">end</span>
|
|
1070
|
+
<span class="ruby-keyword">end</span>
|
|
1071
|
+
<span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">close</span>
|
|
1072
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string('-f')</span>
|
|
1073
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string(@fasta_path)</span>
|
|
1074
|
+
<span class="ruby-comment">#strptrs << FFI::MemoryPointer.from_string(@sam)</span>
|
|
1075
|
+
<span class="ruby-comment">#strptrs << nil</span>
|
|
1076
|
+
|
|
1077
|
+
<span class="ruby-comment"># Now load all the pointers into a native memory block</span>
|
|
1078
|
+
<span class="ruby-comment">#argv = FFI::MemoryPointer.new(:pointer, strptrs.length)</span>
|
|
1079
|
+
<span class="ruby-comment">#strptrs.each_with_index do |p, i|</span>
|
|
1080
|
+
<span class="ruby-comment"># argv[i].put_pointer(0, p)</span>
|
|
1081
|
+
<span class="ruby-comment">#end</span>
|
|
1082
|
+
|
|
1083
|
+
<span class="ruby-comment">#old_stdout = STDOUT.clone</span>
|
|
1084
|
+
<span class="ruby-comment">#read_pipe, write_pipe = IO.pipe()</span>
|
|
1085
|
+
<span class="ruby-comment">#STDOUT.reopen(write_pipe)</span>
|
|
1086
|
+
<span class="ruby-comment">#int bam_mpileup(int argc, char *argv[])</span>
|
|
1087
|
+
<span class="ruby-comment"># Bio::DB::SAM::Tools.bam_mpileup(strptrs.length - 1,argv)</span>
|
|
1088
|
+
<span class="ruby-comment">#if fork</span>
|
|
1089
|
+
<span class="ruby-comment"># write_pipe.close</span>
|
|
1090
|
+
<span class="ruby-comment"># STDOUT.reopen(old_stdout) #beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
|
|
1091
|
+
<span class="ruby-comment"># begin</span>
|
|
1092
|
+
<span class="ruby-comment"># while line = read_pipe.readline</span>
|
|
1093
|
+
<span class="ruby-comment"># yield Pileup.new(line)</span>
|
|
1094
|
+
<span class="ruby-comment"># end</span>
|
|
1095
|
+
<span class="ruby-comment"># rescue EOFError</span>
|
|
1096
|
+
<span class="ruby-comment"># read_pipe.close</span>
|
|
1097
|
+
<span class="ruby-comment"># Process.wait</span>
|
|
1098
|
+
<span class="ruby-comment"># end</span>
|
|
1099
|
+
<span class="ruby-comment">#end</span>
|
|
1100
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1101
|
+
</div><!-- mpileup_plus-source -->
|
|
1102
|
+
|
|
1103
|
+
</div>
|
|
1104
|
+
|
|
1105
|
+
|
|
1106
|
+
|
|
1107
|
+
|
|
1108
|
+
</div><!-- mpileup_plus-method -->
|
|
1109
|
+
|
|
1110
|
+
|
|
1111
|
+
<div id="method-i-open" class="method-detail ">
|
|
1112
|
+
|
|
1113
|
+
<div class="method-heading">
|
|
1114
|
+
<span class="method-name">open</span><span
|
|
1115
|
+
class="method-args">()</span>
|
|
1116
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1117
|
+
</div>
|
|
1118
|
+
|
|
1119
|
+
|
|
1120
|
+
<div class="method-description">
|
|
1121
|
+
|
|
1122
|
+
<p>Function that actually opens the sam file Throws a <a
|
|
1123
|
+
href="SAMException.html">SAMException</a> if the file can’t be open.</p>
|
|
1124
|
+
|
|
1125
|
+
|
|
1126
|
+
|
|
1127
|
+
<div class="method-source-code" id="open-source">
|
|
1128
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 60</span>
|
|
1129
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">open</span>()
|
|
1130
|
+
|
|
1131
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Writing not supported yet"</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@write</span>
|
|
1132
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"No SAM file specified"</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span>
|
|
1133
|
+
|
|
1134
|
+
<span class="ruby-identifier">opts</span> = <span class="ruby-ivar">@write</span> <span class="ruby-operator">?</span> <span class="ruby-string">"w"</span> <span class="ruby-operator">:</span> <span class="ruby-string">"r"</span>
|
|
1135
|
+
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@binary</span> <span class="ruby-keyword">then</span>
|
|
1136
|
+
<span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-string">"b"</span>
|
|
1137
|
+
<span class="ruby-keyword">if</span> <span class="ruby-ivar">@write</span> <span class="ruby-keyword">then</span>
|
|
1138
|
+
<span class="ruby-keyword">unless</span> <span class="ruby-ivar">@compressed</span> <span class="ruby-keyword">then</span>
|
|
1139
|
+
<span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-string">"u"</span>
|
|
1140
|
+
<span class="ruby-keyword">end</span>
|
|
1141
|
+
<span class="ruby-keyword">end</span>
|
|
1142
|
+
<span class="ruby-keyword">end</span>
|
|
1143
|
+
<span class="ruby-identifier">valid</span> = [<span class="ruby-string">"r"</span>, <span class="ruby-string">"w"</span>, <span class="ruby-string">"wh"</span>, <span class="ruby-string">"rb"</span>, <span class="ruby-string">"wb"</span> , <span class="ruby-string">"wbu"</span>]
|
|
1144
|
+
<span class="ruby-keyword">unless</span> <span class="ruby-identifier">valid</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">opts</span>) <span class="ruby-keyword">then</span>
|
|
1145
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"Invalid options for samopen: "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">opts</span>
|
|
1146
|
+
<span class="ruby-keyword">end</span>
|
|
1147
|
+
|
|
1148
|
+
<span class="ruby-identifier">samFile</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">samopen</span>(<span class="ruby-ivar">@sam</span>, <span class="ruby-identifier">opts</span>, <span class="ruby-keyword">nil</span>)
|
|
1149
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">samFile</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword">then</span>
|
|
1150
|
+
<span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword">nil</span>
|
|
1151
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">"File not opened: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
|
|
1152
|
+
<span class="ruby-keyword">end</span>
|
|
1153
|
+
<span class="ruby-ivar">@sam_file</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span><span class="ruby-operator">::</span><span class="ruby-constant">SamfileT</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">samFile</span>)
|
|
1154
|
+
|
|
1155
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1156
|
+
</div><!-- open-source -->
|
|
1157
|
+
|
|
1158
|
+
</div>
|
|
1159
|
+
|
|
1160
|
+
|
|
1161
|
+
|
|
1162
|
+
|
|
1163
|
+
</div><!-- open-method -->
|
|
1164
|
+
|
|
1165
|
+
|
|
1166
|
+
<div id="method-i-query_string" class="method-detail ">
|
|
1167
|
+
|
|
1168
|
+
<div class="method-heading">
|
|
1169
|
+
<span class="method-name">query_string</span><span
|
|
1170
|
+
class="method-args">(chromosome, qstart,qend)</span>
|
|
1171
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1172
|
+
</div>
|
|
1173
|
+
|
|
1174
|
+
|
|
1175
|
+
<div class="method-description">
|
|
1176
|
+
|
|
1177
|
+
<p>Generates a query sting to be used by the region parser in samtools. In
|
|
1178
|
+
principle, you shouldn’t need to use this function.</p>
|
|
1179
|
+
|
|
1180
|
+
|
|
1181
|
+
|
|
1182
|
+
<div class="method-source-code" id="query_string-source">
|
|
1183
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 205</span>
|
|
1184
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
|
|
1185
|
+
<span class="ruby-identifier">query</span> = <span class="ruby-identifier">chromosome</span> <span class="ruby-operator">+</span> <span class="ruby-string">":"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qstart</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-string">"-"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qend</span>.<span class="ruby-identifier">to_s</span>
|
|
1186
|
+
<span class="ruby-identifier">query</span>
|
|
1187
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1188
|
+
</div><!-- query_string-source -->
|
|
1189
|
+
|
|
1190
|
+
</div>
|
|
1191
|
+
|
|
1192
|
+
|
|
1193
|
+
|
|
1194
|
+
|
|
1195
|
+
</div><!-- query_string-method -->
|
|
1196
|
+
|
|
1197
|
+
|
|
1198
|
+
<div id="method-i-to_s" class="method-detail ">
|
|
1199
|
+
|
|
1200
|
+
<div class="method-heading">
|
|
1201
|
+
<span class="method-name">to_s</span><span
|
|
1202
|
+
class="method-args">()</span>
|
|
1203
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1204
|
+
</div>
|
|
1205
|
+
|
|
1206
|
+
|
|
1207
|
+
<div class="method-description">
|
|
1208
|
+
|
|
1209
|
+
<p>Prints a description of the sam file in a text format containg if it is
|
|
1210
|
+
binary or text, the path and the fasta file of the reference</p>
|
|
1211
|
+
|
|
1212
|
+
|
|
1213
|
+
|
|
1214
|
+
<div class="method-source-code" id="to_s-source">
|
|
1215
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 90</span>
|
|
1216
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>()
|
|
1217
|
+
(<span class="ruby-ivar">@binary</span> <span class="ruby-operator">?</span> <span class="ruby-string">"Binary"</span> <span class="ruby-operator">:</span> <span class="ruby-string">"Text"</span>) <span class="ruby-operator">+</span> <span class="ruby-string">" file: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-operator">+</span> <span class="ruby-string">" with fasta: "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
|
|
1218
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1219
|
+
</div><!-- to_s-source -->
|
|
1220
|
+
|
|
1221
|
+
</div>
|
|
1222
|
+
|
|
1223
|
+
|
|
1224
|
+
|
|
1225
|
+
|
|
1226
|
+
</div><!-- to_s-method -->
|
|
1227
|
+
|
|
1228
|
+
|
|
1229
|
+
</section><!-- public-instance-method-details -->
|
|
1230
|
+
|
|
1231
|
+
</section><!-- 5Buntitled-5D -->
|
|
1232
|
+
|
|
1233
|
+
</div><!-- documentation -->
|
|
1234
|
+
|
|
1235
|
+
|
|
1236
|
+
<footer id="validator-badges">
|
|
1237
|
+
<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
|
|
1238
|
+
<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
|
|
1239
|
+
<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
|
|
1240
|
+
</footer>
|
|
1241
|
+
|