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Merge branch 'master' into dev-rmq

This commit is contained in:
Heng Li 2021-05-23 21:01:04 -04:00
parent 9e7247cff9 cd66777bfb
commit 8ec8866100
2 changed files with 5 additions and 4 deletions
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7
README.md
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@ -14,7 +14,8 @@ cd minimap2 && make
# use presets (no test data)
./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio CLR genomic reads
./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads
./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads
./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.18)
./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (GitHub HEAD)
./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads
./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown)
./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam # noisy Nanopore Direct RNA-seq
@ -253,7 +254,7 @@ 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. It has been decided that future tools will
effectively ignore these records. It has been decided that future tools
will seamlessly recognize long-cigar records generated by option `-L`.
**TL;DR**: if you work with ultra-long reads and use tools that only process
@ -274,7 +275,7 @@ CGATCGATAAATAGAGTAG---GAATAGCA
CGATCG---AATAGAGTAGGTCGAATtGCA
```
is represented as `:6-ata:10+gtc:4*at:3`, where `:[0-9]+` represents an
identical block, `-ata` represents a deltion, `+gtc` an insertion and `*at`
identical block, `-ata` represents a deletion, `+gtc` an insertion and `*at`
indicates reference base `a` is substituted with a query base `t`. It is
similar to the `MD` SAM tag but is standalone and easier to parse.

2
python/README.rst
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@ -144,7 +144,7 @@ properties:
* **mlen**: length of the matching bases in the alignment, excluding ambiguous
base matches.
* **NM**: number of mismatches, gaps and ambiguous poistions in the alignment
* **NM**: number of mismatches, gaps and ambiguous positions in the alignment
* **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
reverse strand; 0 if unknown