bam/writer, sam/writer: Validate cigar/sequence/basequalities

[veldsla]

To avoid writing corrupt or incompatible SAM/BAM files an extra validation step is applied before writing. This makes sure:

• The number of base qualities is equal to the sequence length or empty
• The length of the cigar operations matches the sequence length

Closes #59

[veldsla]

This probably needs renaming or moving of stuff. Let me know what you think!

I forgot to edit the async writers. Will update tomorrow!

[zaeleus]

Sorry, this is a bit too out of scope of what was initially suggested in #59. I expected the same logic used in the (BAM) SAM record writer to be ported to the BAM record writer. Can you scale it back to just that?

[veldsla]

I agree the file corruption issue is a different problem from writing sam/bam files that do not conform to the specification. Unfortunately the record writing code is duplicated 6 times. This way the validation is only written twice.

Fixing only the length/corruption issue does not magically make the incompatibility issue go away.

[veldsla]

Apparently using this branch on real world bam files triggers errors, but not in the test suite. Will investigate, converted PR to WIP.

[zaeleus]

Thanks for looking at this in the past. I'm closing this since the alignment parsers/writers have now diverged greatly and makes the same checks.