RubyGems - bio-samtools - Versions diffs - 0.6.2 → 2.0.3 - Mend

bio-samtools 0.6.2 → 2.0.3

Files changed (160) hide show

checksums.yaml +4 -4
data/Gemfile +3 -2
data/README.md +4 -7
data/VERSION +1 -1
data/bio-samtools.gemspec +47 -105
data/doc/Bio.html +68 -131
data/doc/Bio/DB.html +51 -111
data/doc/Bio/DB/Alignment.html +135 -363
data/doc/Bio/DB/Pileup.html +183 -170
data/doc/Bio/DB/SAM.html +1396 -820
data/doc/Bio/DB/SAM/Library.html +73 -123
data/doc/Bio/DB/SAM/Tools.html +51 -273
data/doc/Bio/DB/Tag.html +78 -124
data/doc/Bio/DB/Vcf.html +111 -147
data/doc/LICENSE_txt.html +113 -148
data/doc/created.rid +9 -10
data/doc/fonts.css +167 -0
data/doc/fonts/Lato-Light.ttf +0 -0
data/doc/fonts/Lato-LightItalic.ttf +0 -0
data/doc/fonts/Lato-Regular.ttf +0 -0
data/doc/fonts/Lato-RegularItalic.ttf +0 -0
data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
data/doc/images/add.png +0 -0
data/doc/images/arrow_up.png +0 -0
data/doc/images/delete.png +0 -0
data/doc/images/tag_blue.png +0 -0
data/doc/index.html +48 -54
data/doc/js/darkfish.js +9 -22
data/doc/js/search.js +20 -5
data/doc/js/search_index.js +1 -1
data/doc/rdoc.css +255 -218
data/doc/table_of_contents.html +256 -137
data/ext/Rakefile +57 -0
data/lib/bio-samtools.rb +7 -2
data/lib/bio/BIOExtensions.rb +89 -0
data/lib/bio/db/alignment.rb +59 -0
data/lib/bio/db/fastadb.rb +255 -0
data/lib/bio/db/pileup.rb +221 -172
data/lib/bio/db/sam.rb +639 -589
data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
data/lib/bio/db/vcf.rb +69 -68
data/test/.gitignore +1 -0
data/test/{test_basic.rb → old_test_basic.rb} +33 -1
data/test/samples/small/dupes.bam +0 -0
data/test/samples/small/dupes.sam +274 -0
data/test/samples/small/map_for_reheader.sam +8 -0
data/test/samples/small/map_to_merge1.bam +0 -0
data/test/samples/small/map_to_merge1.bam.bai +0 -0
data/test/samples/small/map_to_merge1.sam +8 -0
data/test/samples/small/map_to_merge2.bam +0 -0
data/test/samples/small/map_to_merge2.bam.bai +0 -0
data/test/samples/small/map_to_merge2.sam +8 -0
data/test/samples/small/no_md.sam +8 -0
data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
data/test/samples/small/test_cov.svg +273 -0
data/test/samples/small/testu.bam.bai +0 -0
data/test/svg +133 -0
data/test/test_pileup.rb +84 -0
data/test/test_sam.rb +331 -0
data/test/test_vcf.rb +11 -0
data/{doc → tutorial}/tutorial.html +0 -0
data/{doc → tutorial}/tutorial.pdf +0 -0
metadata +56 -114
data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
data/doc/Bio/DB/SAMException.html +0 -205
data/doc/LibC.html +0 -155
data/doc/Pileup.html +0 -571
data/doc/Vcf.html +0 -473
data/doc/basic_styles.css +0 -31
data/doc/classes/Bio.html +0 -139
data/doc/classes/Bio/DB.html +0 -137
data/doc/classes/Bio/DB/Alignment.html +0 -441
data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
data/doc/classes/Bio/DB/SAM.html +0 -510
data/doc/classes/Bio/DB/SAM/Library.html +0 -135
data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
data/doc/classes/Bio/DB/SAMException.html +0 -140
data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
data/doc/classes/Bio/DB/Tag.html +0 -160
data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
data/doc/classes/LibC.html +0 -105
data/doc/classes/Pileup.html +0 -374
data/doc/classes/Pileup.src/M000001.html +0 -34
data/doc/classes/Pileup.src/M000002.html +0 -21
data/doc/classes/Pileup.src/M000003.html +0 -21
data/doc/classes/Pileup.src/M000004.html +0 -21
data/doc/classes/Pileup.src/M000005.html +0 -31
data/doc/files/lib/bio-samtools_rb.html +0 -109
data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
data/doc/files/lib/bio/db/sam_rb.html +0 -111
data/doc/fr_class_index.html +0 -43
data/doc/fr_file_index.html +0 -33
data/doc/fr_method_index.html +0 -58
data/doc/lib/bio-samtools_rb.html +0 -115
data/doc/lib/bio/db/pileup_rb.html +0 -171
data/doc/lib/bio/db/sam/bam_rb.html +0 -121
data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
data/doc/lib/bio/db/sam/library_rb.html +0 -115
data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
data/doc/lib/bio/db/sam/sam_rb.html +0 -121
data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
data/doc/lib/bio/db/sam_rb.html +0 -115
data/doc/lib/bio/db/vcf_rb.html +0 -124
data/doc/rdoc-style.css +0 -208
data/lib/bio/db/sam/bam.rb +0 -210
data/lib/bio/db/sam/sam.rb +0 -86
data/test/samples/pipe_char/test.bam +0 -0
data/test/samples/pipe_char/test.bam.bai +0 -0
data/test/samples/pipe_char/test.tam +0 -10
data/test/samples/pipe_char/test_chr.fasta +0 -1000
data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
data/test/samples/small/test +0 -0
data/test/samples/small/test.bam +0 -0
data/test/samples/small/test.fa +0 -20
data/test/samples/small/test.fai +0 -0

@@ -1,31 +0,0 @@
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data/doc/classes/Bio.html DELETED

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-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">is_duplicate</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">is_mapped</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">is_paired</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">isize</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mapq</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mate_strand</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mate_unmapped</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mpos</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">mrnm</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">pos</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">primary</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">qlen</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes pulled with the C library
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">qname</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">qual</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">query_strand</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">query_unmapped</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">rname</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">samstr</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">second_in_pair</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
-documentation) query_strand and mate_strand are true if they are forward.
-It is the opposite to the definition in the BAM format for clarity. primary
-is the negation of is_negative from the BAM format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">seq</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        <tr class="top-aligned-row context-row">
-          <td class="context-item-name">tags</td>
-          <td class="context-item-value">&nbsp;[RW]&nbsp;</td>
-          <td class="context-item-desc">
-Attributes from the format
-</td>
-        </tr>
-        </table>
-      </div>
-    </div>
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Class methods</h3>
-      <div id="method-M000013" class="method-detail">
-        <a name="M000013"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000013.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000013.html');return false;">
-          <span class="method-name">finalize</span><span class="method-args">(object_id)</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-      <div id="method-M000012" class="method-detail">
-        <a name="M000012"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000012.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000012.html');return false;">
-          <span class="method-name">new</span><span class="method-args">()</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-      <h3 class="section-bar">Public Instance methods</h3>
-      <div id="method-M000015" class="method-detail">
-        <a name="M000015"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000015.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000015.html');return false;">
-          <span class="method-name">sam=</span><span class="method-args">(sam)</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-      <div id="method-M000014" class="method-detail">
-        <a name="M000014"></a>
-        <div class="method-heading">
-          <a href="Alignment.src/M000014.html" target="Code" class="method-signature"
-            onclick="popupCode('Alignment.src/M000014.html');return false;">
-          <span class="method-name">set</span><span class="method-args">(bam_alignment, header)</span>
-          </a>
-        </div>
-        <div class="method-description">
-        </div>
-      </div>
-    </div>
-  </div>
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-</body>
-</html>