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BAM unique IDs still don't 100% work #1108

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rbuels opened this Issue Jul 10, 2018 · 3 comments

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rbuels commented Jul 10, 2018

compare http://jbrowse.org/code/JBrowse-1.14.2/?data=%2Ftest%2Fsgn_cram&loc=SL2.50ch03%3A12350002..12350195&tracks=DNA%2Cbam&highlight=

with

samtools view http://jbrowse.org/test/sgn_cram/RNAseq_mapping_def.bam SL2.50ch03:12350002-12350195

there should be 6 features in the bam track, but there are only 2

@rbuels rbuels added the bug label Jul 10, 2018

@rbuels rbuels added this to the 1.15.1 milestone Jul 11, 2018

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rbuels commented Jul 18, 2018

implementation idea: do a crc32 or md5 of the bytes in their stretch of the file. would be relatively fast, but would miss exact duplicate features.

@rbuels rbuels self-assigned this Jul 18, 2018

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cmdcolin commented Jul 26, 2018

The crc32 will get some of the way there but I don't understand these exact duplicate features

Why would these be given the exact same read name and not any differences in flags?

Here is a crc32 test I did

https://github.com/GMOD/jbrowse/compare/hash_bam_features

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cmdcolin commented Jul 26, 2018

With the hash_bam_features branch it returns 4 reads instead of 2 which are on dev and then there are 6 in the bam file

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