update sam writer factory to cope with CRAM file

[ChristinaXu2017]

Description

Our adamajava tools create SAM/BAM outputs by calling org.qcmg.picard.SAMOrBAMWriterFactory, but it won't create CRAM output. Here we update the code but not API, it will make CRAM output if the output file name ending with .cram. The detailed changes are:

• rename SAMOrBAMWriterFactory to SAMWriterFactory
• create a new constructor SAMWriterFactory(..., File reference ), it takes the FASTA reference file and also allows null.
• change method closeWriter() to renameIndex(); Because the writer can automatically close by try clause but our main purpose is to rename the BAM index file from aln.bai to aln.bam.bai and the CRAM index from aln.cram.bai to aln.cram.crai.
• tidy up code:
  • delete some commented out code;
  • move renameIndex(File output) from RenameFile.java to BAMFileUtils.java
  • replace deprecated SAMTagUtils with SAMTag;
  • override FastaRecord.toString(), so the record can output to file.
• use try clause to open/close file reader or writer

Type of change

• [x] New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Existing unit tests are updated and new unit tests for CRAM file is added

Are WDL Updates Required?

No

Checklist:

• [X] My code follows the style guidelines of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] My changes generate no new warnings
• [X] I have added tests that prove my fix is effective or that my feature works
• [X] New and existing unit tests pass locally with my changes

[ChristinaXu2017]

thanks for spotting it, this function only works for renaming, the writer will automatically close by the try block.

[ChristinaXu2017]

The java HTSJDK library creates .bai for bam index; .cram.bai for cram index. The SAMTOOLs c package creates .bam.bai for bam index; .cram.crai for cram index.

It is arguable whether we should follow HTSJDK or SAMTOOLs. I checked "gatk-workflows:five-dollar-genome-analysis-pipeline". It calls "picard.jar SortSam" to create .bai during "ToBam.UnmappedBamToAlignedBam"; however then, it calls SAMTOOLs to index the cram file and then create .cram.crai.

I will run GATK::ApplyBQSR, it can pick up both .bai and .bam.bai; however it throw error if missing index file.