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