Man page - maf-convert(1)

Packages contains this manual

Package:  last-align
apt-get install last-align

Manuals in package:
• maf-cut(1)
• lastdb(1)
• last-train(1)
• last-pair-probs(1)
• last-merge-batches(1)
• maf-join(1)
• lastal(1)
• fasta-nr(1)
• maf-swap(1)
• last-map-probs(1)
• maf-convert(1)
• last-postmask(1)
• fastq-interleave(1)
• maf-sort(1)
• last-split(1)
• last-dotplot(1)
Documentations in package:
• last-align

Manual

MAF-CONVERT

NAME
DESCRIPTION
Usage:
OPTIONS

---

NAME

maf-convert - Convert MAF-format alignments to tabular format

DESCRIPTION

Usage:

maf-convert --help maf-convert axt mafFile(s) maf-convert bed mafFile(s) maf-convert blast mafFile(s) maf-convert blasttab mafFile(s) maf-convert blasttab+ mafFile(s) maf-convert chain mafFile(s) maf-convert gff mafFile(s) maf-convert html mafFile(s) maf-convert psl mafFile(s) maf-convert sam mafFile(s) maf-convert tab mafFile(s)

Read MAF-format alignments & write them in another format.

OPTIONS

-h , --help

show this help message and exit

-s N, --subject = N

which sequence to use as subject/reference

-p , --protein

assume protein alignments, for psl match counts

-j N, --join = N

join consecutive co-linear alignments separated by <= N letters

-J N, --Join = N

join nearest co-linear alignments separated by <= N letters

-n , --noheader

omit any header lines from the output

-d , --dictionary

include dictionary of sequence lengths in sam format

-f DICTFILE, --dictfile = DICTFILE

get sequence dictionary from DICTFILE

-r READGROUP, --readgroup = READGROUP

read group info for sam format

-l LINESIZE, --linesize = LINESIZE

line length for blast and html formats (default: 60)

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