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minor wording changes

This commit is contained in:
Heng Li 2017-10-21 23:46:36 -04:00
parent dc37aee881
commit c6b6392b70
1 changed files with 3 additions and 4 deletions
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README.md
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@ -184,9 +184,8 @@ according to the sequence divergence.
Due to a design flaw, BAM does not work with CIGAR strings with >65535
operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2
may align ~1% of read bases with long CIGARs beyond the capability of BAM. If
you convert such SAM/CRAM to BAM, recent samtools will throw an error and
abort. Older samtools and other tools may even silently create corrupted and
unreadable BAMs.
you convert such SAM/CRAM to BAM, Picard and recent samtools will throw an
error and abort. Older samtools and other tools may create corrupted BAM.
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
@ -197,7 +196,7 @@ 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`.
In summary, if you work with ultra-long reads and use tools that only process
**TD;DR**: if you work with ultra-long reads and use tools that only process
BAM files, please add option `-L`.
#### <a name="cs"></a>The cs optional tag