samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Delete long-term deprecated code #1213

Closed magicDGS closed 5 years ago

magicDGS commented 5 years ago

Description

Closes https://github.com/samtools/htsjdk/issues/955 Closes https://github.com/samtools/htsjdk/issues/972

Checklist

codecov-io commented 5 years ago

Codecov Report

Merging #1213 into master will increase coverage by 0.137%. The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #1213       +/-   ##
===============================================
+ Coverage     68.702%   68.839%   +0.137%     
+ Complexity      8061      8059        -2     
===============================================
  Files            542       540        -2     
  Lines          32711     32640       -71     
  Branches        5533      5523       -10     
===============================================
- Hits           22473     22469        -4     
+ Misses          8038      7969       -69     
- Partials        2200      2202        +2
Impacted Files Coverage Δ Complexity Δ
...samtools/util/AsyncBlockCompressedInputStream.java 72% <0%> (-4%) 12% <0%> (-1%)
...va/htsjdk/samtools/sra/SRAIndexedSequenceFile.java 62.162% <0%> (-2.703%) 6% <0%> (-1%)