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minor wording changes

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Heng Li 2017-10-21 23:38:05 -04:00
parent 37e627aa98
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README.md
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@ -34,7 +34,7 @@ man ./minimap2.1
- [Map short accurate genomic reads](#short-genomic) - [Map short accurate genomic reads](#short-genomic)
- [Full genome/assembly alignment](#full-genome) - [Full genome/assembly alignment](#full-genome)
- [Advanced features](#advanced) - [Advanced features](#advanced)
- [Working CIGARs with >65535 operations in BAM](#long-cigar) - [Working CIGARs with >65535 operations](#long-cigar)
- [The cs optional tag](#cs) - [The cs optional tag](#cs)
- [Evaluation scripts](#eval) - [Evaluation scripts](#eval)
- [Algorithm overview](#algo) - [Algorithm overview](#algo)
@ -179,13 +179,14 @@ according to the sequence divergence.
### <a name="advanced"></a>Advanced features ### <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. Due to a design flaw, BAM does not work with CIGAR strings with >65535
However, aligning ultra-long nanopore reads with minimap2 may align ~1% of read operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2
bases with long CIGARs beyond the capability of BAM. If you convert such SAM to may align ~1% of read bases with long CIGARs beyond the capability of BAM. If
BAM, recent samtools will throw an error and abort. Older samtools and other you convert such SAM/CRAM to BAM, recent samtools will throw an error and
tools may even silently create corrupted and unreadable BAMs. 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. 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 This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR