bio-samtools 0.5.3 → 0.6.0

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Files changed (29) hide show
  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +12 -15
  3. data/doc/Bio.html +7 -7
  4. data/doc/Bio/DB.html +2 -2
  5. data/doc/Bio/DB/Alignment.html +6 -6
  6. data/doc/Bio/DB/Pileup.html +190 -7
  7. data/doc/Bio/DB/SAM.html +58 -22
  8. data/doc/Bio/DB/SAM/Library.html +7 -7
  9. data/doc/Bio/DB/SAM/Tools.html +2 -2
  10. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +2 -2
  11. data/doc/Bio/DB/SAM/Tools/Bam1T.html +2 -2
  12. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +2 -2
  13. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +2 -2
  14. data/doc/Bio/DB/SAM/Tools/SamfileT.html +2 -2
  15. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +2 -2
  16. data/doc/Bio/DB/SAMException.html +3 -3
  17. data/doc/Bio/DB/Tag.html +3 -3
  18. data/doc/Bio/DB/Vcf.html +5 -5
  19. data/doc/LICENSE_txt.html +58 -55
  20. data/doc/LibC.html +2 -2
  21. data/doc/created.rid +7 -7
  22. data/doc/index.html +1 -1
  23. data/doc/js/search_index.js +1 -1
  24. data/doc/lib/bio/db/pileup_rb.html +5 -5
  25. data/doc/table_of_contents.html +19 -9
  26. data/lib/bio/db/pileup.rb +113 -3
  27. data/lib/bio/db/sam.rb +8 -2
  28. data/test/test_basic.rb +9 -0
  29. metadata +67 -22
data/doc/Bio/DB/SAM/Library.html CHANGED
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data/doc/Bio/DB/SAM/Tools.html CHANGED
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data/doc/Bio/DB/SAM/Tools/BamHeaderT.html CHANGED
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data/doc/Bio/DB/SAM/Tools/BamPileup1T.html CHANGED
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data/doc/Bio/DB/SAM/Tools/SamfileT.html CHANGED
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data/doc/Bio/DB/Tag.html CHANGED
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data/doc/Bio/DB/Vcf.html CHANGED
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  <p>Copyright © 2011 Raoul J.P. Bonnal</p>
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  <p>Permission is hereby granted, free of charge, to any person obtaining a
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+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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  <p>to take away your freedom to share and change the works. By contrast, the
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- for all its users. We, the Free Software Foundation, use the GNU General
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- Public License for most of our software; it applies also to any other work
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- released this way by its authors. You can apply it to your programs, too.</p>
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+ and change all versions of a program–to make sure it remains free
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+ software for all its users. We, the Free Software Foundation, use the GNU
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+ General Public License for most of our software; it applies also to any
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+ other work released this way by its authors. You can apply it to your
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- modification of the work as a means of enforcing, against the work’s users,
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  <p>works, which are not by their nature extensions of the covered work, and
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  which are not combined with it such as to form a larger program, in or on a
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- volume of a storage or distribution medium, is called an “aggregate” if the
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- compilation and its resulting copyright are not used to limit the access or
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- legal rights of the compilation’s users beyond what the individual works
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- permit. Inclusion of a covered work in an aggregate does not cause this
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- License to apply to the other parts of the aggregate.</p>
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+ volume of a storage or distribution medium, is called an “aggregate” if
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+ the compilation and its resulting copyright are not used to limit the
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+ access or legal rights of the compilation’s users beyond what the
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+ individual works permit. Inclusion of a covered work in an aggregate does
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+ not cause this License to apply to the other parts of the aggregate.</p>
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  <pre>6. Conveying Non-Source Forms.
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@@ -456,13 +458,13 @@ conveying the object code work.</p>
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  household purposes, or (2) anything designed or sold for incorporation into
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  a dwelling. In determining whether a product is a consumer product,
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  doubtful cases shall be resolved in favor of coverage. For a particular
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- product received by a particular user, “normally used” refers to a typical
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- or common use of that class of product, regardless of the status of the
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- particular user or of the way in which the particular user actually uses,
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- or expects or is expected to use, the product. A product is a consumer
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- product regardless of whether the product has substantial commercial,
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- industrial or non-consumer uses, unless such uses represent the only
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- significant mode of use of the product.</p>
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+ product received by a particular user, “normally used” refers to a
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+ typical or common use of that class of product, regardless of the status of
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+ the particular user or of the way in which the particular user actually
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+ uses, or expects or is expected to use, the product. A product is a
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+ consumer product regardless of whether the product has substantial
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+ commercial, industrial or non-consumer uses, unless such uses represent the
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+ only significant mode of use of the product.</p>
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  <pre>&quot;Installation Information&quot; for a User Product means any methods,</pre>
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@@ -669,9 +671,9 @@ the contents of its contributor version.</p>
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  <p>agreement or commitment, however denominated, not to enforce a patent (such
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  as an express permission to practice a patent or covenant not to sue for
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- patent infringement). To “grant” such a patent license to a party means to
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- make such an agreement or commitment not to enforce a patent against the
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- party.</p>
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+ patent infringement). To “grant” such a patent license to a party
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+ means to make such an agreement or commitment not to enforce a patent
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+ against the party.</p>
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  <pre>If you convey a covered work, knowingly relying on a patent license,</pre>
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@@ -682,10 +684,10 @@ you must either (1) cause the Corresponding Source to be so available, or
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  (2) arrange to deprive yourself of the benefit of the patent license for
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  this particular work, or (3) arrange, in a manner consistent with the
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  requirements of this License, to extend the patent license to downstream
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- recipients. “Knowingly relying” means you have actual knowledge that, but
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- for the patent license, your conveying the covered work in a country, or
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- your recipient’s use of the covered work in a country, would infringe one
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- or more identifiable patents in that country that you have reason to
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+ recipients. “Knowingly relying” means you have actual knowledge that,
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+ but for the patent license, your conveying the covered work in a country,
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+ or your recipient’s use of the covered work in a country, would infringe
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+ one or more identifiable patents in that country that you have reason to
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  believe are valid.</p>
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  <pre>If, pursuant to or in connection with a single transaction or</pre>
@@ -762,9 +764,9 @@ Foundation.</p>
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  <pre>If the Program specifies that a proxy can decide which future</pre>
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- <p>versions of the GNU General Public License can be used, that proxy’s public
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- statement of acceptance of a version permanently authorizes you to choose
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- that version for the Program.</p>
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+ <p>versions of the GNU General Public License can be used, that proxy’s
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+ public statement of acceptance of a version permanently authorizes you to
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+ choose that version for the Program.</p>
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  <pre>Later license versions may give you additional or different</pre>
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@@ -776,12 +778,12 @@ or copyright holder as a result of your choosing to follow a later version.</p>
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  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY</pre>
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  <p>APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
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- HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY
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- OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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- PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
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- IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
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- ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
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+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT
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+ WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
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+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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+ PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
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+ THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME
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+ THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
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  <pre>16. Limitation of Liability.
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@@ -848,14 +850,15 @@ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
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  This is free software, and you are welcome to redistribute it
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  under certain conditions; type `show c' for details.</pre>
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- <p>The hypothetical commands `show w’ and `show c’ should show the appropriate
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- parts of the General Public License. Of course, your program’s commands
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- might be different; for a GUI interface, you would use an “about box”.</p>
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+ <p>The hypothetical commands `show w’ and `show c’ should show the
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+ appropriate parts of the General Public License. Of course, your
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+ program’s commands might be different; for a GUI interface, you would use
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+ an “about box”.</p>
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  <pre>You should also get your employer (if you work as a programmer) or school,</pre>
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- <p>if any, to sign a “copyright disclaimer” for the program, if necessary. For
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- more information on this, and how to apply and follow the GNU GPL, see
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+ <p>if any, to sign a “copyright disclaimer” for the program, if necessary.
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+ For more information on this, and how to apply and follow the GNU GPL, see
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  &lt;<a href="http://www.gnu.org/licenses/">www.gnu.org/licenses/</a>&gt;.</p>
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  <pre>The GNU General Public License does not permit incorporating your program</pre>
@@ -872,7 +875,7 @@ href="http://www.gnu.org/philosophy/why-not-lgpl.html">www.gnu.org/philosophy/wh
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