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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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Proposed replacement for progress PR #1302

Closed yfarjoun closed 5 years ago

yfarjoun commented 5 years ago

This PR is a replacement for #1180. it adds the feature that the read-name printing is only turned on after the logger notices 1000 incidents where the position was decreasing.

More exactly: The logger keep a counter that increments when the position is decreasing and vice versa (but remains non-negative) If this counter is greater than 1000, the logger will also emit read-names.

codecov-io commented 5 years ago

Codecov Report

Merging #1302 into master will increase coverage by 1.657%. The diff coverage is 67.647%.

@@               Coverage Diff               @@
##              master     #1302       +/-   ##
===============================================
+ Coverage     67.644%   69.301%   +1.657%     
- Complexity      8188      9321     +1133     
===============================================
  Files            560       563        +3     
  Lines          33462     36757     +3295     
  Branches        5635      6502      +867     
===============================================
+ Hits           22635     25473     +2838     
- Misses          8644      8958      +314     
- Partials        2183      2326      +143
Impacted Files Coverage Δ Complexity Δ
src/main/java/htsjdk/samtools/util/Log.java 59.016% <33.333%> (ø) 17 <0> (ø) :arrow_down:
...a/htsjdk/samtools/util/AbstractProgressLogger.java 53.425% <70.968%> (+10.832%) 13 <8> (+6) :arrow_up:
...ava/htsjdk/samtools/cram/structure/CramHeader.java 41.026% <0%> (-6.974%) 9% <0%> (+2%)
.../main/java/htsjdk/samtools/util/ftp/FTPClient.java 17.094% <0%> (-6.077%) 7% <0%> (+1%)
.../java/htsjdk/samtools/util/IntervalListWriter.java 86.364% <0%> (-1.636%) 4% <0%> (-1%)
...java/htsjdk/samtools/cram/structure/Container.java 93.636% <0%> (-1.1%) 28% <0%> (+15%)
...c/main/java/htsjdk/samtools/util/IntervalList.java 73.585% <0%> (-0.834%) 129% <0%> (+55%)
src/main/java/htsjdk/samtools/util/Interval.java 63.043% <0%> (-0.593%) 50% <0%> (+24%)
...va/htsjdk/samtools/SAMSequenceDictionaryCodec.java 86.957% <0%> (-0.543%) 12% <0%> (+6%)
...ain/java/htsjdk/samtools/util/MergingIterator.java 85.417% <0%> (-0.298%) 18% <0%> (+7%)
... and 62 more
yfarjoun commented 5 years ago

@lbergelson this is ready for a review...