a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/lib/splatAli.c src/lib/splatAli.c index 10e29c9..dcd9809 100644 --- src/lib/splatAli.c +++ src/lib/splatAli.c @@ -1,235 +1,234 @@ /* splatAli.c was originally generated by the autoSql program, which also * generated splatAli.h and splatAli.sql. This module links the database and * the RAM representation of objects. */ /* This file is copyright 2008 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ #include "common.h" #include "linefile.h" #include "dystring.h" #include "sqlNum.h" #include "sqlList.h" #include "splatAli.h" -static char const rcsid[] = "$Id: splatAli.c,v 1.3 2008/11/06 05:07:06 kent Exp $"; void splatAliStaticLoad(char **row, struct splatAli *ret) /* Load a row from splatAli table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->chrom = row[0]; ret->chromStart = sqlSigned(row[1]); ret->chromEnd = sqlSigned(row[2]); ret->alignedBases = row[3]; ret->score = sqlSigned(row[4]); safecpy(ret->strand, sizeof(ret->strand), row[5]); ret->readName = row[6]; } struct splatAli *splatAliLoad(char **row) /* Load a splatAli from row fetched with select * from splatAli * from database. Dispose of this with splatAliFree(). */ { struct splatAli *ret; AllocVar(ret); ret->chrom = cloneString(row[0]); ret->chromStart = sqlSigned(row[1]); ret->chromEnd = sqlSigned(row[2]); ret->alignedBases = cloneString(row[3]); ret->score = sqlSigned(row[4]); safecpy(ret->strand, sizeof(ret->strand), row[5]); ret->readName = cloneString(row[6]); return ret; } struct splatAli *splatAliLoadAll(char *fileName) /* Load all splatAli from a whitespace-separated file. * Dispose of this with splatAliFreeList(). */ { struct splatAli *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileRow(lf, row)) { el = splatAliLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct splatAli *splatAliLoadAllByChar(char *fileName, char chopper) /* Load all splatAli from a chopper separated file. * Dispose of this with splatAliFreeList(). */ { struct splatAli *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = splatAliLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct splatAli *splatAliCommaIn(char **pS, struct splatAli *ret) /* Create a splatAli out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new splatAli */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->chrom = sqlStringComma(&s); ret->chromStart = sqlSignedComma(&s); ret->chromEnd = sqlSignedComma(&s); ret->alignedBases = sqlStringComma(&s); ret->score = sqlSignedComma(&s); sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); ret->readName = sqlStringComma(&s); *pS = s; return ret; } void splatAliFree(struct splatAli **pEl) /* Free a single dynamically allocated splatAli such as created * with splatAliLoad(). */ { struct splatAli *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freeMem(el->alignedBases); freeMem(el->readName); freez(pEl); } void splatAliFreeList(struct splatAli **pList) /* Free a list of dynamically allocated splatAli's */ { struct splatAli *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; splatAliFree(&el); } *pList = NULL; } void splatAliOutput(struct splatAli *el, FILE *f, char sep, char lastSep) /* Print out splatAli. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chrom); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%d", el->chromStart); fputc(sep,f); fprintf(f, "%d", el->chromEnd); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->alignedBases); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%d", el->score); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->strand); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->readName); if (sep == ',') fputc('"',f); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ int splatAliCmpReadName(const void *va, const void *vb) /* Compare two based on readName. Also separate secondarily on chrom position. */ { const struct splatAli *a = *((struct splatAli **)va); const struct splatAli *b = *((struct splatAli **)vb); int diff = strcmp(a->readName, b->readName); if (diff == 0) diff = a->chromStart - b->chromStart; if (diff == 0) diff = a->chromEnd - b->chromEnd; if (diff == 0) diff = a->strand - b->strand; if (diff == 0) diff = strcmp(a->chrom, b->chrom); return diff; } int splatAliScore(char *ali) /* Score splat-encoded alignment. */ { int score = 0; char c; while ((c = *ali++)) { switch (c) { case 'a': case 'c': case 'g': case 't': score -= 2; break; case 'A': case 'C': case 'G': case 'T': score += 2; break; case 'n': case 'N': break; case '^': score -= 3; ali += 1; break; case '-': score -= 3; break; } } return score; } void splatAliLookForBest(struct splatAli *start, struct splatAli *end, int *retBestScore, int *retBestCount) /* Scan through list from start up to but not including end (which may be NULL) * and figure out best score and number of elements in list with that score. */ { int bestScore = 0, bestCount = 0; struct splatAli *el; for (el = start; el != end; el = el->next) { int score = splatAliScore(el->alignedBases); if (score >= bestScore) { if (score > bestScore) { bestScore = score; bestCount = 1; } else bestCount += 1; } } *retBestScore = bestScore; *retBestCount = bestCount; }