Allow the use of getSAMString on SAMReadGroupRecord objects

[Lenbok]

Description

Fairly minor, this just allows programmatic access to the string representation of a read group, in much the same way as SAMRecord.getSAMString(). AFAIK there currently isn't really a non-convoluted way to get this. This is useful for displaying to the end user a problematic SAM read group.

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)

[nh13]

Did you build a time machine, out of a DeLorean? - 2009

[Lenbok]

Haha! (Copied an existing test file from the same package as the starting point and the comment was folded in the editor off the bat! I can update if you want)

[codecov-io]

Codecov Report

Merging #827 into master will increase coverage by 0.002%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master      #827       +/-   ##
===============================================
+ Coverage     64.865%   64.868%   +0.002%     
- Complexity      7189      7194        +5     
===============================================
  Files            527       527               
  Lines          31769     31774        +5     
  Branches        5424      5424               
===============================================
+ Hits           20607     20611        +4     
+ Misses          9015      9014        -1     
- Partials        2147      2149        +2

Impacted Files	Coverage Δ	Complexity Δ
.../java/htsjdk/samtools/AbstractSAMHeaderRecord.java	57.143% <ø> (ø)	7 <0> (ø)	⬇️
.../main/java/htsjdk/samtools/SAMTextHeaderCodec.java	79.31% <100%> (+0.955%)	44 <4> (+3)	⬆️
src/main/java/htsjdk/samtools/SAMFileHeader.java	59.184% <100%> (+0.28%)	34 <0> (+1)	⬆️
...c/main/java/htsjdk/samtools/SAMSequenceRecord.java	68.293% <100%> (+0.391%)	31 <1> (+1)	⬆️
.../main/java/htsjdk/samtools/SAMReadGroupRecord.java	50% <100%> (+0.877%)	17 <1> (+1)	⬆️
...rc/main/java/htsjdk/samtools/SAMProgramRecord.java	75.676% <100%> (+6.231%)	15 <1> (+2)	⬆️
...sjdk/samtools/util/Md5CalculatingOutputStream.java	71.795% <0%> (-7.692%)	8% <0%> (-1%)
.../htsjdk/samtools/SAMRecordQueryNameComparator.java	40.741% <0%> (-7.407%)	7% <0%> (-2%)
...dk/samtools/seekablestream/SeekableHTTPStream.java	54.545% <0%> (-1.515%)	9% <0%> (-1%)
...a/htsjdk/samtools/cram/encoding/rans/Decoding.java	85.714% <0%> (+3.571%)	12% <0%> (+1%)	⬆️
... and 1 more

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[yfarjoun]

looks good @Lenbok. This is a good idea.

Could you do the same refactoring for the 3 other classes that inherit from AbstractSAMHeaderRecord and add an abstract getSAMString() function to AbstractSAMHeaderRecord?

[lbergelson]

@Lenbok This seems like a good idea and the implementation + test seems good. It seems like a good idea for all of the other types of header lines as well. If you don't mind, could you make toSAMString into an abstract method on AbstractSAMHeaderRecord and do analogous implementations for the other subclasses?

[Lenbok]

@yfarjoun, @lbergelson No probs, done. I didn't construct an explicit new test for SAMFileHeader.getSAMString(), as that one is essentially refactored out of the existing clone() method, which already gets called all over the show.

[lbergelson]

@Lenbok Thanks you! 👍