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Hard clipping causes incorrect BAM mismatch display #1513

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cmdcolin opened this issue Jun 6, 2020 · 2 comments
Closed

Hard clipping causes incorrect BAM mismatch display #1513

cmdcolin opened this issue Jun 6, 2020 · 2 comments

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@cmdcolin
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cmdcolin commented Jun 6, 2020

I haven't fully confirmed but there are incorrect mismatches being displayed and I'm fairly certain it's due to hardclipping in BAM the mismatches are displayed incorrectly

jbrowse org_code_JBrowse-1 16 9__data=sample_data%2Fjson%2Fvolvox loc=ctgA%3A26194 26262 tracks=volvox-long_reads%2Cvolvox-long_reads-cram highlight=

Can be seen with supplementary alignments enabled on the volvox long reads sample track
@cmdcolin
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cmdcolin commented Jun 6, 2020

affects jb2 since has same logic. I think the logic should probably be (a) unit tested a bit and (b) performance improved :) something I started on jb2 but this type of bugfix will need porting back to jb1

@cmdcolin
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cmdcolin commented Jun 6, 2020

Note that via samtools tview and looking at the bases, T is the correct one

@cmdcolin cmdcolin mentioned this issue Jun 6, 2020
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@cmdcolin cmdcolin closed this as completed Jun 7, 2020
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