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Check if input BAM files are sorted by coordinate #19

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tjakobi opened this issue Jul 27, 2016 · 0 comments
Closed

Check if input BAM files are sorted by coordinate #19

tjakobi opened this issue Jul 27, 2016 · 0 comments
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DCC version 0.4.4

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tjakobi commented Jul 27, 2016

Currently DCC assumes the BAM files are sorted. In case they are not, pysam will eventually crash.

[bam_pileup_core] the input is not sorted (reads out of order) [bam_plp_destroy] memory leak: 1. Continue anyway.
@tjakobi tjakobi added the bug label Jul 27, 2016
@tjakobi tjakobi added this to the DCC version 0.4.4 milestone Jul 27, 2016
@tjakobi tjakobi self-assigned this Jul 27, 2016
tjakobi added a commit that referenced this issue Aug 5, 2016
@tjakobi
Fixes #19
e391e76 
DCC now checks if a) BAM files have an index and if so, b) if they are sorted. This is done by getting the first 100 read mapping positions and check if they are in order. Should be good enough for government use. DCC throws an user readable error message and exceptions should all be caught.
@tjakobi tjakobi closed this as completed Aug 5, 2016
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