4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c index af8cfd7..2622c74 100644 --- src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c +++ src/hg/chimpStuff/chimpHiQualDiffs/chimpHiQualDiffs.c @@ -1,224 +1,224 @@ /* chimpHiQualDiffs - Create list of chimp high quality differences. */ /* Copyright (C) 2011 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "qaSeq.h" #include "axt.h" #include "portable.h" #include "rle.h" void usage() /* Explain usage and exit. */ { errAbort( "chimpHiQualDiffs - Create list of chimp high quality differences\n" "usage:\n" " chimpHiQualDiffs axtDir chimp.qac out.bed\n" "options:\n" " -winSize Window Size (11)\n" " -diffQualMin Min quality score for difference (30)\n" " -winQualMin Min quality score for window (25)\n" " -winMaxDiff Maximum number of differences in window (0)\n" " -indelOk Allow indels in window (currently not implemented)\n" " -ignore98 Do not allow chimp quality score of 98 for difference\n" " -chimpPos Print chimp positions in addition to human positions\n" "output format:\n" " humanChrom humanStart humanEnd humanBase chimpBase [chimpChrom chimpStart chimpEnd]\n" ); } static struct optionSpec options[] = { {"winSize", OPTION_INT}, {"diffQualMin", OPTION_INT}, {"winQualMin", OPTION_INT}, {"winMaxDiff", OPTION_INT}, {"indelOk", OPTION_BOOLEAN}, {"ignore98", OPTION_BOOLEAN}, {"chimpPos", OPTION_BOOLEAN}, {NULL, 0} }; struct qac /* A run-length-compressed set of quality scores. */ { int uncSize; /* Uncompressed size. */ int compSize; /* Compressed size. */ signed char data[1]; /* Compressed data. */ }; struct hash *qacReadToHash(char *fileName) /* Read in a qac file into a hash of qacs keyed by name. */ { boolean isSwapped; FILE *f = qacOpenVerify(fileName, &isSwapped); bits32 compSize, uncSize; struct qac *qac; char *name; struct hash *hash = newHash(18); int count = 0; for (;;) { name = readString(f); if (name == NULL) break; mustReadOne(f, uncSize); if (isSwapped) uncSize = byteSwap32(uncSize); mustReadOne(f, compSize); if (isSwapped) compSize = byteSwap32(compSize); qac = needHugeMem(sizeof(*qac) + compSize - 1); qac->uncSize = uncSize; qac->compSize = compSize; mustRead(f, qac->data, compSize); hashAdd(hash, name, qac); ++count; } carefulClose(&f); printf("Read %d qacs from %s\n", count, fileName); return hash; } void axtHiQualDiffs(char *axtFile, struct hash *qacHash, FILE *f) /* Write out high quality diffs in axtFile to f. */ { char *qName = cloneString(""); UBYTE *qQuals = NULL; UBYTE *quals = NULL; struct qac *qac = NULL; struct axt *axt = NULL; struct lineFile *lf = lineFileOpen(axtFile, TRUE); int qStart, qDir, qPos, qWinStart, qWinEnd, tPos; int qWinSize = optionInt("winSize", 11); int qQualMin = optionInt("diffQualMin", 30); int qWinQualMin = optionInt("winQualMin", 25); int qWinMaxDiff = optionInt("winMaxDiff", 2); boolean qIndelOk = optionExists("indelOk"); boolean qIgnore98 = optionExists("ignore98"); boolean chimpPos = optionExists("chimpPos"); int qHalfWinSize = qWinSize/2; while ((axt = axtRead(lf)) != NULL) { char *qSym = axt->qSym, *tSym = axt->tSym; int symIx, symCount = axt->symCount; char qc,tc; toUpperN(qSym, symCount); toUpperN(tSym, symCount); if (!sameString(axt->qName, qName)) { freez(&qName); qName = cloneString(axt->qName); qac = hashMustFindVal(qacHash, qName); freez(&qQuals); qQuals = needHugeMem(qac->uncSize); rleUncompress(qac->data, qac->compSize, qQuals, qac->uncSize); } if (axt->qStrand == '+') { qStart = axt->qStart; qDir = 1; } else { qStart = qac->uncSize - axt->qStart - 1; qDir = -1; } qPos = qStart; tPos = axt->tStart; for (symIx = 0; symIx < symCount; ++symIx) { qc = qSym[symIx]; tc = tSym[symIx]; if (qc == '-') tPos += 1; else if (tc == '-') qPos += qDir; else { if (qc != tc) { qWinStart = qPos - qHalfWinSize; qWinEnd = qWinStart + qWinSize; if (qWinStart >= 0 && qWinEnd < qac->uncSize) { if (qQuals[qPos] >= qQualMin) { int i; boolean ok = TRUE; for (i = qWinStart; i<qWinEnd; ++i) if (qQuals[i] < qWinQualMin) { ok = FALSE; break; } if (ok) { int diffCount = 0; int symWinStart = symIx - qHalfWinSize; int symWinEnd = symWinStart + qWinSize; for (i=symWinStart; i < symWinEnd; ++i) { qc = qSym[i]; tc = tSym[i]; if (qc == '-' || tc == '-') { ok = FALSE; break; } if (qc != tc) ++diffCount; } if (ok && diffCount <= qWinMaxDiff && (!qIgnore98 || qQuals[qPos] != 98) ) { if (chimpPos) fprintf(f, "%s\t%d\t%d\t%c\t%c\t%s\t%d\t%d\n", axt->tName, tPos, tPos+1, tSym[symIx], qSym[symIx], axt->qName, qPos, qPos+1); else fprintf(f, "%s\t%d\t%d\t%c\t%c\n", axt->tName, tPos, tPos+1, tSym[symIx], qSym[symIx]); } } } } } qPos += qDir; tPos += 1; } } axtFree(&axt); } lineFileClose(&lf); } void chimpHiQualDiffs(char *axtDir, char *qacName, char *bedName) /* chimpHiQualDiffs - Create list of chimp high quality differences. */ { struct hash *qacHash = qacReadToHash(qacName); struct fileInfo *axtEl, *axtList = listDirX(axtDir, "*.axt", TRUE); FILE *f = mustOpen(bedName, "w"); if (axtList==NULL) axtList = listDirX(axtDir, "*.axt.gz", TRUE); if (axtList==NULL) printf("No axt files were found in the '%s' directory.\n",axtDir); for (axtEl = axtList; axtEl != NULL; axtEl = axtEl->next) axtHiQualDiffs(axtEl->name, qacHash, f); carefulClose(&f); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); chimpHiQualDiffs(argv[1], argv[2], argv[3]); return 0; }