CRAM input handling

[alkaZeltser]

Notes on CRAM input handling

@tyamaguchi-ucla

PipeVal

CRAM inputs do not pass PipeVal, likely due to inability to detect reference files associated with the CRAM.
May need to modify something so that the reference fasta is also provided to PipeVal alongside CRAM.

Picard CollectHsMetrics

This tool fails with the following exception:

 Exception in thread "main" java.lang.IllegalArgumentException: Failure getting reference bases for sequence chr1
        at htsjdk.samtools.cram.build.CRAMReferenceRegion.fetchReferenceBasesByRegion(CRAMReferenceRegion.java:172)
        at htsjdk.samtools.cram.build.CRAMReferenceRegion.fetchReferenceBasesByRegion(CRAMReferenceRegion.java:192)
        at htsjdk.samtools.cram.structure.Slice.normalizeCRAMRecords(Slice.java:450)
        at htsjdk.samtools.cram.structure.Container.getSAMRecords(Container.java:322)
        at htsjdk.samtools.CRAMIterator.nextContainer(CRAMIterator.java:112)
        at htsjdk.samtools.CRAMIterator.hasNext(CRAMIterator.java:204)
        at htsjdk.samtools.SamReader$AssertingIterator.hasNext(SamReader.java:608)
        at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:155)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:289)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:104)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:114)

By default CollectHsMetrics is not given a reference file. Providing the fasta file (and making sure the index file is also mounted in the same directory) solves this error.
param:
--REFERENCE_SEQUENCE $reference_fasta