Mf get read position from ref

[fleharty]

Description

Adding functionality to optionally include softclips in getAlignmentBlocks

Things to think about before submitting:

• [ ] Make sure your changes compile and new tests pass locally.
• [ ] Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• [ ] Extended the README / documentation, if necessary
• [ ] Check your code style.
• [ ] Write a clear commit title and message
  • The commit message should describe what changed and is targeted at htsjdk developers
  • Breaking changes should be mentioned in the commit message.

[tfenne]

@fleharty I really don't like this - it adds a bunch more public methods to SAMRecord for something that is rather questionable. If you really want to treat soft clips as Ms I feel like the more correct thing to do would be to update the cigar on the record, and then use the existing getReadPositionAtRefPosition() method(s).

[codecov-io]

Codecov Report

Merging #1475 into master will increase coverage by 0.005%. The diff coverage is 78.571%.

@@               Coverage Diff               @@
##              master     #1475       +/-   ##
===============================================
+ Coverage     69.203%   69.207%   +0.005%     
- Complexity      8701      8709        +8     
===============================================
  Files            588       588               
  Lines          34581     34596       +15     
  Branches        5779      5785        +6     
===============================================
+ Hits           23931     23943       +12     
- Misses          8368      8369        +1     
- Partials        2282      2284        +2     

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/SAMUtils.java	62.972% <77.778%> (+0.170%)	136.000 <7.000> (+5.000)
src/main/java/htsjdk/samtools/SAMRecord.java	68.148% <80.000%> (-0.175%)	299.000 <5.000> (+2.000)	:arrow_down:
...samtools/util/AsyncBlockCompressedInputStream.java	76.000% <0.000%> (+4.000%)	13.000% <0.000%> (+1.000%)

[fleharty]

@tfenne That's an interesting idea. I'll try to accomplish this by modifying the CIGAR. Thanks.

[fleharty]

Closing this PR, I believe there is a better solution.