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add seqs to cram features #1149
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
The way I did it was in the cramjs test suite I wrote a little script that made sure I got the same sequences as the samtools SAM dumps of the cram files…
On Tue, Jul 31, 2018 at 1:20 PM Colin Diesh ***@***.***> wrote: I guess on second thought directly comparing BAM to CRAM seems unnecessary as long as compared to some objective samtools output or something — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#1149 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEgFYncFLwVN5yuVEK86XZ8g0-__Nlmks5uMLwHgaJpZM4Vo7yP> .
Does that have any consequences for JBrowse right now?