This is the equivalent of halRenameGenomes but for MAF/TAF.
You pass the 2-column TSV to taffy view via the new -n option, and it will rename the contig names in the alingment block accordingly.
. characters get special treatment consistent with an <assembly>.<contig> naming scheme.
So if the mapping has hg38 -> Homo_sapiens then hg38.chr1 would get renamed to Homo_sapiens.chr1 etc. The naming also applies to input regions via the taffy view -r option. So if the MAF/TAF is indexed along hg38, then you can search for Homo_sapiens.chr1:10-100 via the name map.
The goal for this is to make working with TAF/MAF files that use accessions for assembly names .
Since both the assembly and contig names can have "."s in them, it uses a a greedy resolver, scanning dots from left to right to find one that makes a prefix that's in the input map.
This is the equivalent of
halRenameGenomesbut for MAF/TAF.You pass the 2-column TSV to
taffy viewvia the new-noption, and it will rename the contig names in the alingment block accordingly..characters get special treatment consistent with an<assembly>.<contig>naming scheme.So if the mapping has
hg38 -> Homo_sapiensthenhg38.chr1would get renamed toHomo_sapiens.chr1etc. The naming also applies to input regions via thetaffy view -roption. So if the MAF/TAF is indexed along hg38, then you can search forHomo_sapiens.chr1:10-100via the name map.The goal for this is to make working with TAF/MAF files that use accessions for assembly names .
Since both the assembly and contig names can have "."s in them, it uses a a greedy resolver, scanning dots from left to right to find one that makes a prefix that's in the input map.