Converts MAF alignments in another format.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
maf{:bash}
:file
Multiple Alignment Format (MAF) file, optionally compressed with gzip
*.{maf.gz,maf}
format{:bash}
:string
Output format (one of axt, bam, blast, blasttab, cram, chain, gff, html, psl, sam, or tab)
meta2{:bash}
fasta{:bash}
Genome file in FASTA format for CRAM conversion. If compressed it must be done in BGZF format (like with the bgzip tool).
*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}
meta3{:bash}
fai{:bash}
Genome index file needed for CRAM conversion.
*.fai
meta4{:bash}
gzi{:bash}
Genome index file needed for CRAM conversion when the genome file was compressed with the BGZF algorithm.
*.gzi
meta5{:bash}
dict{:bash}
Samtools dictionary of the genome file.
*.dict
axt_gz{:bash}
*.axt.gz{:bash}
Gzipped pairwise alignment in Axt (Blastz) format (optional)
*.axt.gz
bam{:bash}
*.bam{:bash}
Pairwise alignment in BAM format (optional)
*.bam
bed_gz{:bash}
*.bed.gz{:bash}
Gzipped pairwise alignment in BED format (optional)
*.bed.gz
blast_gz{:bash}
*.blast.gz{:bash}
Gzipped pairwise alignment in blast format (optional)
*.blast.gz
blasttab_gz{:bash}
*.blasttab.gz{:bash}
Gzipped pairwise alignment in blasttab format (optional)
*.blasttab.gz
chain_gz{:bash}
*.chain.gz{:bash}
Gzipped pairwise alignment in UCSC chain format (optional)
*.chain.gz
cram{:bash}
*.cram{:bash}
Pairwise alignment in CRAM format (optional)
*.cram
gff_gz{:bash}
*.gff.gz{:bash}
Gzipped pairwise alignment in GFF format (optional)
*.gff.gz
html_gz{:bash}
*.html.gz{:bash}
Gzipped pairwise alignment in HTML format (optional)
*.html.gz
psl_gz{:bash}
*.psl.gz{:bash}
Gzipped pairwise alignment in PSL (BLAT) format (optional)
*.psl.gz
sam_gz{:bash}
*.sam.gz{:bash}
Gzipped pairwise alignment in SAM format (optional)
*.sam.gz
tab_gz{:bash}
*.tab.gz{:bash}
Gzipped pairwise alignment in TAB format (optional)
*.tab.gz
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
LAST finds & aligns related regions of sequences.
