maf-convert1

Convert maf-format alignments to tabular format

Overview

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)

Releases

8 releases since Debian 6.0 (Squeeze); the text changed 7 times.

--Join since Debian 11 (Bullseye); --dictfile since Debian 8 (Jessie); --dictionary since Debian 7 (Wheezy); --join since Debian 9 (Stretch); --linesize since Debian 7 (Wheezy); --noheader since Debian 8 (Jessie); --protein since Debian 7 (Wheezy); --readgroup since Debian 8 (Jessie); --subject since Debian 12 (Bookworm); -J since Debian 11 (Bullseye); -d since Debian 7 (Wheezy); -f since Debian 8 (Jessie); -j since Debian 9 (Stretch); -l since Debian 7 (Wheezy); -n since Debian 8 (Jessie); -p since Debian 7 (Wheezy); -r since Debian 8 (Jessie); -s since Debian 12 (Bookworm).