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add seqs to cram features #1149

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merged 4 commits into from Jul 31, 2018

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rbuels commented Jul 31, 2018

fixes #1126

@rbuels rbuels requested a review from cmdcolin Jul 31, 2018

@wafflebot wafflebot bot added the in progress label Jul 31, 2018

@cmdcolin cmdcolin force-pushed the 1126_cram_seq branch from 5227655 to a62493c Jul 31, 2018

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cmdcolin commented Jul 31, 2018

This looks like the sequence is obtained perfectly. If possible it would be cool to programmatically compare the seq of some reads from BAM and CRAM. The long reads are sort of a nice gauntlet for that comparison

Otherwise I manually compared a couple sequences from some select long reads on both the BAM and CRAM track and they were the same

One inconsistency that should be resolved still is that the mismatches structure between CRAM and BAM is slightly different

Specifically, the "insertion" mismatches of BAM don't store the sequence and CRAM does, and vice versa, the "deletion" of BAM stores the base but CRAM doesn't

Kind of a weird thing

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cmdcolin commented Jul 31, 2018

I guess on second thought directly comparing BAM to CRAM seems unnecessary as long as compared to some objective samtools output or something

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rbuels commented Jul 31, 2018

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rbuels commented Jul 31, 2018

One inconsistency that should be resolved still is that the mismatches structure between CRAM and BAM is slightly different

Specifically, the "insertion" mismatches of BAM don't store the sequence and CRAM does, and vice versa, the "deletion" of BAM stores the base but CRAM doesn't

Does that have any consequences for JBrowse right now?

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cmdcolin commented Jul 31, 2018

@rbuels currently renderAlignments on CRAM is bad due to a bad assumption made on mismatches data structure for BAM basically but otherwise it's fine

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cmdcolin commented Jul 31, 2018

Alright I see what happened, CRAM was able to detect actual insertion base pairs for some cases. I think it should be fixed now

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cmdcolin commented Jul 31, 2018

LGTM :)

@cmdcolin cmdcolin merged commit 23c722e into dev Jul 31, 2018

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@wafflebot wafflebot bot removed the in progress label Jul 31, 2018

@cmdcolin cmdcolin deleted the 1126_cram_seq branch Aug 6, 2018

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