Fix #1049

[danking]

Description

Fixes #1049, return value of FastaSequenceIndexEntry.getIndexEntry is unusable.

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[danxmoran]

Hi @danking, you'll need to move FastaSequenceIndexEntry to its own file to get this to compile.

[pshapiro4broad]

Hi @danking, you'll need to move FastaSequenceIndexEntry to its own file to get this to compile.

Given the way this class is used, making it a static inner class might be a better option. If the inner class was called Entry then you'd refer to it as FastaSequenceIndex.Entry.

[danking]

@danxmoran hah sorry, too much time in Scala land.

I'll move it since that seems to be the lowest impact change.

[danking]

@danxmoran I think this will compile.

[codecov-io]

Codecov Report

Merging #1072 into master will not change coverage.
The diff coverage is 74.074%.

@@             Coverage Diff             @@
##              master     #1072   +/-   ##
===========================================
  Coverage     66.154%   66.154%           
- Complexity      7609      7618    +9     
===========================================
  Files            533       534    +1     
  Lines          32373     32373           
  Branches        5509      5508    -1     
===========================================
  Hits           21416     21416           
  Misses          8792      8792           
  Partials        2165      2165

Impacted Files	Coverage Δ	Complexity Δ
.../htsjdk/samtools/reference/FastaSequenceIndex.java	59.42% <ø> (-4.121%)	12 <0> (ø)
...dk/samtools/reference/FastaSequenceIndexEntry.java	74.074% <74.074%> (ø)	9 <9> (?)
...sjdk/samtools/util/Md5CalculatingOutputStream.java	69.231% <0%> (-7.692%)	8% <0%> (-1%)
...samtools/util/AsyncBlockCompressedInputStream.java	76% <0%> (+4%)	13% <0%> (+1%)	⬆️

[danxmoran]

LGTM, over to @jacarey for another look & merge

[jacarey]

Pinging @lbergelson @tfenne for objections to merge.

[lbergelson]

👍