- Make get/set attributes methods take a SAMTag input

[yfarjoun]

... so that callers do not need to adorn their code with useless .name() or .getBinaryTag() calls.

• remove superfluous .name() and .getBinaryTag() calls

Description

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

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.

[yfarjoun]

@pshapiro4broad you inspired me to do this....

[lbergelson]

Oh man, I've wanted to do this for a long time but I've been too lazy.

[lbergelson]

Oh man, I've wanted to do this for a long time but I've been too lazy. The thing we MIGHT want to do is make it return a typed value when given a tag with a known type. Thats more work though.

[yfarjoun]

wouldn't that require having separate enums for the different types?

On Wed, Apr 15, 2020 at 11:18 AM Louis Bergelson notifications@github.com wrote:

Oh man, I've wanted to do this for a long time but I've been too lazy. The thing we MIGHT want to do is make it return a typed value when given a tag with a known type. Thats more work though.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/samtools/htsjdk/pull/1472#issuecomment-614102479, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAU6JURIVNIZJOLQQXX3ROLRMXF55ANCNFSM4MIU37SA .

[lbergelson]

yes, until http://openjdk.java.net/jeps/301 releases in ???

[lbergelson]

@yfarjoun This is waiting on an update to the comment about avoiding redundant conversion in SAMRecord.hasAttribute and friends.

[codecov-commenter]

Codecov Report

Merging #1472 into master will increase coverage by 0.391%. The diff coverage is 60.000%.

@@               Coverage Diff               @@
##              master     #1472       +/-   ##
===============================================
+ Coverage     69.205%   69.596%   +0.391%     
- Complexity      8700      9066      +366     
===============================================
  Files            587       601       +14     
  Lines          34580     36212     +1632     
  Branches        5779      6088      +309     
===============================================
+ Hits           23931     25202     +1271     
- Misses          8367      8664      +297     
- Partials        2282      2346       +64     

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/htsjdk/samtools/SAMUtils.java	62.802% <33.333%> (ø)	131.000 <1.000> (ø)
...c/main/java/htsjdk/samtools/util/SequenceUtil.java	70.118% <33.333%> (ø)	130.000 <18.000> (ø)
src/main/java/htsjdk/samtools/SAMRecord.java	67.433% <41.667%> (-0.890%)	303.000 <11.000> (+6.000)	:arrow_down:
...main/java/htsjdk/samtools/SAMRecordSetBuilder.java	89.591% <68.750%> (ø)	75.000 <0.000> (ø)
src/main/java/htsjdk/samtools/SamPairUtil.java	57.488% <70.588%> (ø)	20.000 <0.000> (ø)
.../java/htsjdk/samtools/AbstractSAMHeaderRecord.java	75.000% <100.000%> (+3.571%)	9.000 <1.000> (+1.000)
.../htsjdk/samtools/SAMRecordQueryNameComparator.java	92.593% <100.000%> (ø)	21.000 <0.000> (ø)
...rc/main/java/htsjdk/samtools/SamFileValidator.java	84.211% <100.000%> (ø)	82.000 <3.000> (ø)
.../main/java/htsjdk/samtools/fastq/FastqEncoder.java	89.744% <100.000%> (ø)	17.000 <1.000> (ø)
src/main/java/htsjdk/samtools/util/CigarUtil.java	53.571% <100.000%> (ø)	4.000 <0.000> (ø)
... and 40 more