Change to support CRAM

[keiranmraine]

If VerifyBamId adds CRAM support remove dependancy on Bio::DB::Sam and switch to Bio::DB::HTS.

This will then be fully BAM/CRAM agnostic.

• Add cram support as below
• Hotfix/1.4.3 #21 / Sample meta validate input: leading or tailing spaces in file paths are kept in output, error should be raised or remove spaces #20 - old hotfix needs pulling into this feature.
• Upgrade verifyBamId #14 - Upgrade of underlying verifyBamId - Also in dockstore-cgpmap
• Errors when no SNP coverage #19 - div by zero issues

Modify the perl wrapper to sample the relevant locations from an input CRAM to a temporary BAM:

samtools view -F 3844 -L loci.bed -q 10 -b orig.cram | tee new.bam | samtools index - > new.bam.bai

Make the applied flags obvious in code:

4 - read unmapped (0x4)
256 - not primary alignment (0x100)
512 - read fails platform/vendor quality checks (0x200)
1024 - read is PCR or optical duplicate (0x400)
2048 - supplementary alignment (0x800)

[keiranmraine]

Investigate suggestion here:

statgen/verifyBamID#2