2b563cb9c48b6c8a7f8774cd229f9129d16e8a19 markd Wed Jun 14 13:49:05 2023 -0700 fixed typo in help message diff --git src/utils/pslMap/usage.txt src/utils/pslMap/usage.txt index 6708eec..f5075e4 100644 --- src/utils/pslMap/usage.txt +++ src/utils/pslMap/usage.txt @@ -29,33 +29,33 @@ Options: -chainMapFile - mapFile is a chain file instead of a psl file -swapMap - swap query and target sides of map file. -swapIn - swap query and target sides of inPsl file. -suffix=str - append str to the query ids in the output alignment. Useful with protein alignments, where the result is not actually and alignment of the protein. -keepTranslated - if either psl is translated, the output psl will be translated (both strands explicted). Normally an untranslated psl will always be created -mapFileWithInQName - The first column of the mapFile PSL records are a qName, the remainder is a standard PSL. When an inPsl record is mapped, only mapping records are used with the corresponding qName. -inType=type - input alignment type (prot-port, prot-na, na-na) - This is the type swapping if -swapIn is supplied. + This is the type after swapping if -swapIn is supplied. -mapType=type - map alignment type (prot-port, prot-na, na-na) - This is the type swapping if -swapMap is supplied. + This is the type after swapping if -swapMap is supplied. -mapInfo=file - output a file with information about each mapping. The file has the following columns: o srcQName, srcQStart, srcQEnd, srcQSize - qName, etc of psl being mapped (source alignment) o srcTName, srcTStart, srcTEnd - tName, etc of psl being mapped o srcStrand - strand of psl being mapped o srcAligned - number of aligned based in psl being mapped o mappingQName, mappingQStart, mappingQEnd - qName, etc of mapping psl used to map alignment o mappingTName, mappingTStart, mappingTEnd - tName, etc of mapping psl o mappingStrand - strand of mapping psl o mappingId - chain id, or psl file row o mappedQName mappedQStart, mappedQEnd - qName, etc of