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Changing htsjdk to produce sam version 1.6 #1211

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merged 4 commits into from
Nov 7, 2018
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  • Htsjdk has techinically been producing Sam version 1.6 since support for long cigars was added.
  • Updating that list of acceptable versions to include 1.6 and setting the header version of new bams to 1.6

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)

* Htsjdk has techinically been producing Sam version 1.6 since support for long cigars was added.
* Updating that list of acceptable versions to include 1.6 and setting the header version of new bams to 1.6
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codecov-io commented Oct 26, 2018

Codecov Report

Merging #1211 into master will increase coverage by 0.095%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #1211       +/-   ##
===============================================
+ Coverage     68.702%   68.796%   +0.095%     
- Complexity      8061      8094       +33     
===============================================
  Files            542       542               
  Lines          32711     32887      +176     
  Branches        5533      5577       +44     
===============================================
+ Hits           22473     22625      +152     
- Misses          8038      8054       +16     
- Partials        2200      2208        +8
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/SAMFileHeader.java 64.623% <100%> (-3.641%) 54 <1> (+9)
...samtools/util/AsyncBlockCompressedInputStream.java 72% <0%> (-4%) 12% <0%> (-1%)
...va/htsjdk/samtools/sra/SRAIndexedSequenceFile.java 62.162% <0%> (-2.703%) 6% <0%> (-1%)
.../main/java/htsjdk/samtools/SAMTextHeaderCodec.java 87.668% <0%> (+6.263%) 72% <0%> (+25%) ⬆️
...sjdk/samtools/util/Md5CalculatingOutputStream.java 74.359% <0%> (+7.692%) 8% <0%> (+1%) ⬆️

pshapiro4broad and others added 2 commits November 5, 2018 14:06
Co-Authored-By: lbergelson <louisb@broadinstitute.org>
Co-Authored-By: lbergelson <louisb@broadinstitute.org>
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@cmnbroad cmnbroad left a comment

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The changes themselves look fine. The only question I have is whether there are any special cases we need to consider when merging old headers with 1.6 headers ? Otherwise LGTM.

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cmnbroad commented Nov 5, 2018

👍 to taking this and addressing #1202 separately.

@lbergelson lbergelson merged commit 393f2c0 into master Nov 7, 2018
@lbergelson lbergelson deleted the lb_add_sam_1.6 branch November 7, 2018 19:04
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5 participants