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r550: fixed -L issues with secondary and supp aln

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Heng Li
2017-11-04 12:13:38 -04:00
parent 52ffbc9e0c
commit a3f0aa1d5b
3 changed files with 8 additions and 7 deletions
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README.md
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@@ -212,10 +212,8 @@ To avoid this issue, you can add option `-L` at the minimap2 command line.
This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR
at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and
sorting) still work with such BAM records; tools that read CIGAR will
effectively ignore these records. I have pull requests to the SAM spec, htslib,
htsjdk, bedtools2, Rsamtools and igv.js. If they are accepted, future versions
of these tools will seamlessly recognize long-cigar records generated by option
`-L`.
effectively ignore these records. It has been decided that future tools will
will seamlessly recognize long-cigar records generated by option `-L`.
**TD;DR**: if you work with ultra-long reads and use tools that only process
BAM files, please add option `-L`.