Fix unmapped secondary alignments#592
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These are ignored when comparing the outputs, but it allows us to test whether the BAM output is valid (according to picard ValidateSamFile).
Is-new-baseline: yes
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When secondary alignments are enabled, we currently handle unmapped reads incorrectly. So for example, if we have a pair where R1 can be mapped and has multiple mappings but R2 cannot be mapped, we output these SAM records:
I first changed it so that the second time R2 is output it is also marked as secondary, but then we have a SAM record that is both unmapped and secondary, which
picard ValidateSamFilerightfully complains about. The correct solution seems to be to just not output that last record, which is what this PR does.Also, we now let strobealign generate secondary alignments within the baseline comparison script. They are ignored when actually comparing the records to the baseline version, but this allows us to run
ValidateSamFileon a file with secondary alignments.The last commit changes the baseline commit because running strobealign with
-N 5and ignoring all secondary alignments does not give the same results as running it with-N 0.