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)

maf-convert 1609                                  February 2025                                   MAF-CONVERT(1)