670aea936b66579839b921640e0be7de5985b87b kent Wed Mar 6 14:40:46 2013 -0800 Fixed bug where the empty string was always making it look like one monomer was missing. diff --git src/kehayden/alphaAsm/alphaAsm.c src/kehayden/alphaAsm/alphaAsm.c index a697bae..77875ed 100644 --- src/kehayden/alphaAsm/alphaAsm.c +++ src/kehayden/alphaAsm/alphaAsm.c @@ -1654,31 +1654,31 @@ struct monomer *monomer; for (monomer = monomerList; monomer != NULL; monomer = monomer->next) monomer->outCount = 0; /* Increase output count each time a monomer is used. */ struct dlNode *node; for (node = ll->head; !dlEnd(node); node = node->next) { monomer = node->val; monomer->outCount += 1; } /* Count up unused. */ int missing = 0; for (monomer = monomerList; monomer != NULL; monomer = monomer->next) - if (monomer->outCount == 0) + if (monomer->outCount == 0 && !sameString(monomer->word, "")) missing += 1; return missing; } void alphaAsm(char *readsFile, char *monomerOrderFile, char *outFile) /* alphaAsm - assemble alpha repeat regions such as centromeres from reads that have * been parsed into various repeat monomer variants. Cycles of these variants tend to * form higher order repeats. */ { /* This routine reads in the input, and then calls a routine that produces the * output for a given size. If not all monomers are included in the output, then it * will try to find the minimum output size needed to include all monomers. */ /* Read in inputs, and put in "store" */