9543454d80c5c9ad8096398fba715c07ae8801b4 markd Mon May 11 12:23:22 2020 -0700 fixed usage message diff --git src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c index 237a8ca..eb949c5 100644 --- src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c +++ src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c @@ -17,31 +17,31 @@ * - Must dealt with block structure that is different than the source genePred. TransMap * may split or merge blocks. This builds a genePred with the number of blocks generated * by intersecting the two block structures and then packs the genePred at the end. * - Strand may have changed, so this must be handled with all query coordinates. */ void usage() /* Explain usage and exit. */ { errAbort( "transMapPslToGenePred - convert PSL alignments of mRNAs to gene annotations.\n" "\n" "usage:\n" - " mrnaToGene [options] sourceGenePred mappedPsl mappedGenePred\n" + " transMapPslToGenePred [options] sourceGenePred mappedPsl mappedGenePred\n" "\n" "Convert PSL alignments from transmap to genePred. It specifically handles\n" "alignments where the source genes are genomic annotations in genePred\n" "format, that are converted to PSL for mapping and using this program to\n" "create a new genePred.\n" "\n" "This is an alternative to mrnaToGene which determines CDS and frame from\n" "the original annotation, which may have been imported from GFF/GTF. This\n" "was created because the genbankCds structure use by mrnaToGene doesn't\n" "handle partial start/stop codon or programmed frame shifts. This requires\n" "handling the list of CDS regions and the /codon_start attribute, At some\n" "point, this program may be extended to do handle genbank alignments correctly.\n" "\n" "Options:\n"