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minor wording changes

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Heng Li 2017-10-21 23:38:05 -04:00
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README.md
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@ -34,7 +34,7 @@ man ./minimap2.1
- [Map short accurate genomic reads](#short-genomic)
- [Full genome/assembly alignment](#full-genome)
- [Advanced features](#advanced)
- [Working CIGARs with >65535 operations in BAM](#long-cigar)
- [Working CIGARs with >65535 operations](#long-cigar)
- [The cs optional tag](#cs)
- [Evaluation scripts](#eval)
- [Algorithm overview](#algo)
@ -179,13 +179,14 @@ according to the sequence divergence.
### <a name="advanced"></a>Advanced features
#### <a name="long-cigar"></a>Working CIGARs with >65535 operations in BAM
#### <a name="long-cigar"></a>Working CIGARs with >65535 operations
At present, BAM does not work with CIGAR strings with >65535 operations.
However, aligning ultra-long nanopore reads with minimap2 may align ~1% of read
bases with long CIGARs beyond the capability of BAM. If you convert such SAM to
BAM, recent samtools will throw an error and abort. Older samtools and other
tools may even silently create corrupted and unreadable BAMs.
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.
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