samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Yf add platforms #1427

Closed yfarjoun closed 4 years ago

yfarjoun commented 5 years ago

Adding legal values for the PL tag of the @rg SAM header line (BGI and OTHER)

codecov-io commented 5 years ago

Codecov Report

Merging #1427 into master will increase coverage by 0.086%. The diff coverage is 85.714%.

@@               Coverage Diff               @@
##              master     #1427       +/-   ##
===============================================
+ Coverage     68.118%   68.204%   +0.086%     
- Complexity      8381      8591      +210     
===============================================
  Files            573       573               
  Lines          33988     34407      +419     
  Branches        5669      5753       +84     
===============================================
+ Hits           23152     23467      +315     
- Misses          8646      8734       +88     
- Partials        2190      2206       +16
Impacted Files Coverage Δ Complexity Δ
.../main/java/htsjdk/samtools/SAMReadGroupRecord.java 93.333% <85.714%> (-0.952%) 48 <0> (ø)
src/main/java/htsjdk/samtools/util/CodeUtil.java 70% <0%> (-1.429%) 6% <0%> (+2%)
src/main/java/htsjdk/variant/vcf/VCFHeader.java 88.889% <0%> (-1.227%) 113% <0%> (+37%)
src/main/java/htsjdk/tribble/util/FTPHelper.java 0% <0%> (ø) 0% <0%> (ø) :arrow_down:
...main/java/htsjdk/tribble/util/RemoteURLHelper.java 46.667% <0%> (+0.513%) 4% <0%> (+1%) :arrow_up:
...n/java/htsjdk/variant/vcf/VCFContigHeaderLine.java 82.609% <0%> (+2.053%) 16% <0%> (+5%) :arrow_up:
...rc/main/java/htsjdk/tribble/util/ParsingUtils.java 77.734% <0%> (+2.871%) 88% <0%> (+44%) :arrow_up:
src/main/java/htsjdk/samtools/util/IOUtil.java 61.862% <0%> (+3.448%) 238% <0%> (+118%) :arrow_up:
...samtools/util/AsyncBlockCompressedInputStream.java 76% <0%> (+4%) 13% <0%> (+1%) :arrow_up:
src/main/java/htsjdk/tribble/util/HTTPHelper.java 55% <0%> (+7.083%) 5% <0%> (+1%) :arrow_up:
... and 1 more
yfarjoun commented 4 years ago

not sure why...afterall, we have things that are not in the spec (like sortorder=duplicate)