samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Made toIntervalList an iterator as well ... #1455

Closed yfarjoun closed 4 years ago

yfarjoun commented 4 years ago

So that large VCFs can be turned into intervalLists by operating on them in a stream rather than loading all the intervals into memory.

Description

Please explain the changes you made here. Explain the motivation for making this change. What existing problem does the pull request solve?

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codecov-io commented 4 years ago

Codecov Report

Merging #1455 into master will increase coverage by 0.019%. The diff coverage is 91.176%.

@@              Coverage Diff               @@
##             master     #1455       +/-   ##
==============================================
+ Coverage     68.41%   68.429%   +0.019%     
- Complexity     8499      8505        +6     
==============================================
  Files           583       584        +1     
  Lines         34413     34478       +65     
  Branches       5729      5730        +1     
==============================================
+ Hits          23542     23593       +51     
- Misses         8650      8665       +15     
+ Partials       2221      2220        -1
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/tribble/MutableFeature.java 100% <100%> (ø) 6 <6> (?)
...c/main/java/htsjdk/samtools/util/IntervalList.java 73.333% <86.842%> (+1.153%) 59 <0> (-5) :arrow_down:
...rc/main/java/htsjdk/variant/vcf/VCFFileReader.java 66.667% <93.75%> (-0.498%) 30 <6> (+8)
src/main/java/htsjdk/samtools/util/Interval.java 66.667% <0%> (-1.667%) 26% <0%> (-3%)
yfarjoun commented 4 years ago

Thanks for the review @lbergelson. back to you.