088074eea1a818698e3d3fa20a15da8fb56a06c6 markd Tue Jan 18 20:19:22 2011 -0800 fixed typos in help message and made it more detailed diff --git src/hg/genePredToGtf/genePredToGtf.c src/hg/genePredToGtf/genePredToGtf.c index 16dd84f..9fcfa32 100644 --- src/hg/genePredToGtf/genePredToGtf.c +++ src/hg/genePredToGtf/genePredToGtf.c @@ -14,33 +14,34 @@ /* Explain usage and exit. */ { errAbort( "genePredToGtf - Convert genePred table or file to gtf.\n" "usage:\n" " genePredToGtf database genePredTable output.gtf\n" "If database is 'file' then track is interpreted as a file\n" "rather than a table in database.\n" "options:\n" " -utr - Add 5UTR and 3UTR features\n" " -honorCdsStat - use cdsStartStat/cdsEndStat when defining start/end\n" " codon records\n" " -source=src set source name to uses\n" " -addComments - Add comments before each set of transcript records.\n" " allows for easier visual inspection\n" - "Note: use refFlat (tables only) or extended genePred file/table to include\n" - "geneName. If you are using genePred with starts with a numeric bin number,\n" - "drop it using the UNIX cut command:\n" + "Note: use a refFlat table or extended genePred table or file to include\n" + "the gene_name attribute in the output. This will not work with a refFlat\n" + "table dump file. If you are using a genePred file that starts with a numeric\n" + "bin column, drop it using the UNIX cut command:\n" " cut -f 2- in.gp | genePredToGtf file stdin out.gp\n" ); } /* FIXME: * - right now, if not using -honorCdsStat and the CDS is not a multiple of * three, a start_codon is written but not a stop_codon. This is * deceptive. Should really not output either, maybe add a comment. */ static struct optionSpec options[] = { {"utr", OPTION_BOOLEAN}, {"honorCdsStat", OPTION_BOOLEAN}, {"source", OPTION_STRING}, {"addComments", OPTION_BOOLEAN},