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Test for chromap failing #291
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The command that the pipeline uses for aligning reads with
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After discussion in Slack with @lextallan seems here seems that the problem is the TLEN column in the files produced by |
This has been partially fixed in #290 by filtering out paired-end data when Chromap is used. However, once a new version of Chromap is released that output usable bam files, this issue might need to be revisited. |
Some update: TLEN is recently added into Chromap's SAM output in the latest release. |
Thanks for the update @swiftgenomics will give it a try! |
Closes in #338 |
The test for chromap are failing with the exception below:
To me, it seems like the fragment size can not be correctly obtained from the bam files. However, the test with the small dataset work with the rest of the aligners (
BWA
,STAR
andBowtie2
). The problem seems to be related to the pairing of the reads performed bychromap
since I have run the full test withchromap
(there we have single-end reads) without encountering this problem.The text was updated successfully, but these errors were encountered: