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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 isRefOnlyBlock function... #1215

Closed jsotobroad closed 5 years ago

jsotobroad commented 5 years ago

Description

to VariantContext so we can check whether or not it is a ref block according the VCF v4.3 spec.

Checklist

jsotobroad commented 5 years ago

@yfarjoun could you take a look at this

codecov-io commented 5 years ago

Codecov Report

Merging #1215 into master will increase coverage by 0.617%. The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #1215       +/-   ##
===============================================
+ Coverage     68.712%   69.329%   +0.617%     
- Complexity      8062      8104       +42     
===============================================
  Files            542       543        +1     
  Lines          32728     32477      -251     
  Branches        5537      5500       -37     
===============================================
+ Hits           22488     22516       +28     
+ Misses          8041      7753      -288     
- Partials        2199      2208        +9
Impacted Files Coverage Δ Complexity Δ
.../htsjdk/variant/variantcontext/VariantContext.java 77.586% <100%> (+0.13%) 244 <4> (+4) :arrow_up:
...ain/java/htsjdk/variant/variantcontext/Allele.java 77.206% <100%> (+0.34%) 88 <3> (+3) :arrow_up:
src/main/java/htsjdk/samtools/SAMTagUtil.java 0% <0%> (-96.078%) 0% <0%> (-6%)
...n/java/htsjdk/samtools/cram/common/IntHashMap.java 0% <0%> (-47.253%) 0% <0%> (-10%)
.../htsjdk/samtools/cram/structure/AlignmentSpan.java 72.727% <0%> (-9.416%) 11% <0%> (+1%)
...sjdk/samtools/util/Md5CalculatingOutputStream.java 66.667% <0%> (-7.692%) 7% <0%> (-1%)
...samtools/cram/encoding/readfeatures/Insertion.java 31.818% <0%> (-7.071%) 4% <0%> (ø)
...ava/htsjdk/samtools/cram/structure/CramHeader.java 40% <0%> (-4.444%) 7% <0%> (ø)
src/main/java/htsjdk/tribble/index/Block.java 56.25% <0%> (-3.75%) 6% <0%> (ø)
...amtools/cram/encoding/readfeatures/InsertBase.java 65% <0%> (-3.421%) 7% <0%> (ø)
... and 168 more
jsotobroad commented 5 years ago

One question about comments, rest of the changes should have been made

jsotobroad commented 5 years ago

@pshapiro4broad @yfarjoun I think I got everything answered/changed that was asked for

jsotobroad commented 5 years ago

nit picked!