hts-specs
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samtools
SAM/VCF Strict draft
PR for discussing proposed SAM Strict rule changes. Work in progress continuing from #281 discussion.
@jkbonfield I'd rather not expand this particular PR to include changes to the SAM specs themselves. My PR does appear to be highlighting some issues with SAMv1.5 that have avoided scrutiny, but I think the best course of action is to get a SAM v1.5 strict document and validator implementation based on the v1.5 specifications before updating the specs.
That's fine - I can accept that as an order in which things are done. Yes I think there are problems with the spec which haven't been spotted as no one has really gone over it with such a fine tooth-comb before. Thank you for doing this.
Could you do me a favor and include the pdf in these commits? when we get to the end you can remove the pdf and compile it "correctly" for the sake of having the PDF versioned.
I was wondering if we want the error "code" to not have spaces in it. This will help when we want to run a validation tool on the commandline and specify which codes to ignore. Spaces will mean that every code needs to be surrounded by quotes. COULD_WE_USE_THIS_FORMAT_FOR_CODES? (not shouting, just suggesting!)
The TeX is invalid at the moment, meaning a PDF cannot currently be produced.
I'm not a TeX expert, but it looks like you need eg \vfifteen instead of \v15 commands and braces around the {\tt text} sections. There are some other minor things like \bam not being defined too. I tried correcting this and have a pdf that builds now, although it's formatted wrong and becomes pure fixed-width after a while.
The version in https://github.com/jkbonfield/hts-specs/tree/strict builds now, but needs a lot of formatting still. I'm not planning on doing this myself - this was just a test to see how to get it in a readable format.
Any discussion or review comments on SAM and VCF strictness proposals are naturally separate. Would it not be more practical to open a VCF strict proposal as a new separate PR?
I agree with a comment from @jmarshall above about splitting this into two. Since in its current form it concerns both VCF and SAM, I've added the appropriate labels for the time being
