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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Add support for SQ-AN in SAMSequenceDictionary #956 #1474

Closed yfarjoun closed 4 years ago

yfarjoun commented 4 years ago

This is a replacement of PR #956

see discussion and comments there....

one major difference from that PR:

codecov-commenter commented 4 years ago

Codecov Report

Merging #1474 into master will increase coverage by 0.329%. The diff coverage is 76.471%.

@@               Coverage Diff               @@
##              master     #1474       +/-   ##
===============================================
+ Coverage     69.235%   69.563%   +0.329%     
- Complexity      8721      9012      +291     
===============================================
  Files            588       601       +13     
  Lines          34620     35983     +1363     
  Branches        5787      6033      +246     
===============================================
+ Hits           23969     25031     +1062     
- Misses          8367      8603      +236     
- Partials        2284      2349       +65
Impacted Files Coverage Δ Complexity Δ
.../main/java/htsjdk/samtools/SAMValidationError.java 96.154% <ø> (ø) 9.000 <0.000> (ø)
...c/main/java/htsjdk/samtools/SAMSequenceRecord.java 78.333% <75.000%> (-3.000%) 50.000 <36.000> (+11.000) :arrow_down:
...in/java/htsjdk/samtools/SAMSequenceDictionary.java 75.000% <88.889%> (+1.761%) 46.000 <3.000> (+1.000)
...c/main/java/htsjdk/tribble/gff/SequenceRegion.java 80.556% <0.000%> (-1.797%) 14.000% <0.000%> (+7.000%) :arrow_down:
...ava/htsjdk/samtools/util/htsget/HtsgetRequest.java 61.905% <0.000%> (ø) 34.000% <0.000%> (?%)
.../util/htsget/HtsgetMalformedResponseException.java 28.571% <0.000%> (ø) 1.000% <0.000%> (?%)
.../java/htsjdk/samtools/util/htsget/HtsgetClass.java 100.000% <0.000%> (ø) 1.000% <0.000%> (?%)
...va/htsjdk/samtools/util/htsget/HtsgetResponse.java 91.176% <0.000%> (ø) 8.000% <0.000%> (?%)
src/main/java/htsjdk/io/HtsPath.java 51.316% <0.000%> (ø) 15.000% <0.000%> (?%)
...sjdk/samtools/util/htsget/HtsgetErrorResponse.java 80.000% <0.000%> (ø) 4.000% <0.000%> (?%)
... and 26 more
yfarjoun commented 4 years ago

back to you @lbergelson