13324df7d810e3cd1d64d93e8f83de7f7611e473 hiram Fri Sep 25 18:55:52 2026 -0700 claude found and error in the code and added a test for the bug refs #34360 diff --git src/utils/pafToPsl/pafToPsl.c src/utils/pafToPsl/pafToPsl.c index bceab7ac11f..68eef244f4c 100644 --- src/utils/pafToPsl/pafToPsl.c +++ src/utils/pafToPsl/pafToPsl.c @@ -1,327 +1,335 @@ /* pafToPsl - converting paf output from minimap2 into UCSC psl format. * This is a conversion on permission from author: Chenxi Zhou from code * in the Gene Myers project: fastGA/FASTGA utility PAFtoPSL * https://github.com/thegenemyers/FASTGA * to function in the kent C code environment. */ #include "common.h" #include "linefile.h" #include "options.h" #include "psl.h" #include "sqlNum.h" #include "hash.h" #include "obscure.h" #include <ctype.h> void usage() /* Explain usage and exit. */ { errAbort( "pafToPsl - converting paf output from minimap2 into UCSC psl format\n" "usage:\n" " pafToPsl in.paf out.psl\n" "options:\n" " -cigarTag=tag SAM-style tag that carries the alignment CIGAR string\n" " (default cg:Z:). The CIGAR is made of M/=/X, I and D\n" " operators, as minimap2 writes it.\n" " -tSizes=file.chrom.sizes Tab-separated <name><size> file. When given,\n" " each record's target size is taken from here instead of\n" " the PAF's own tSize column; a target name missing from\n" " this file causes that record to be skipped with a\n" " warning, and a size that disagrees with the PAF is\n" " also warned about (this file's value wins).\n" " -qSizes=file.chrom.sizes Same as -tSizes, for the query side.\n" "out.psl may be \"stdout\" to write to standard output.\n" "### Thank you to Chenxi Zhou for permission to translate the original ###\n" "### PAFtoPSL code from the Gene Myers project: FASTGA ###\n" "### https://github.com/thegenemyers/FASTGA ###\n" "### into this kent C code implementation. ###" ); } static char *cigarTag = "cg:Z:"; static char *tSizesFile = NULL; static char *qSizesFile = NULL; /* Command line validation table. */ static struct optionSpec options[] = { {"cigarTag", OPTION_STRING}, {"tSizes", OPTION_STRING}, {"qSizes", OPTION_STRING}, {NULL, 0}, }; static void pushBlock(struct psl *psl, int *blockSpace, int qPos, int tPos, int size) /* Append one ungapped alignment block to psl, growing the block arrays if * needed. */ { if (psl->blockCount >= *blockSpace) pslGrow(psl, blockSpace); psl->qStarts[psl->blockCount] = qPos; psl->tStarts[psl->blockCount] = tPos; psl->blockSizes[psl->blockCount] = size; psl->blockCount++; } static boolean cigarToPsl(struct psl *psl, int *blockSpace, char *cigar, char *fileName, int lineIx) /* Parse a CIGAR string (as found in a PAF cg:Z: tag) into psl's alignment * blocks, and fill in the fields that are derived from it: the trimmed * qStart/qEnd/tStart/tEnd, the insert counts, misMatch and nCount. * psl->match must already be set from the PAF record's own match count. * Returns FALSE, after printing a warning, if the CIGAR is inconsistent * with psl's alignment range. */ { int qNumInsert = 0, qBaseInsert = 0, tNumInsert = 0, tBaseInsert = 0; int qPos = 0, tPos = 0, lens = 0, insl = 0, insr = 0, opLen = 0; char *c = cigar; char op, prevOp = '\0'; int i; psl->blockCount = 0; while (*c != '\0') { opLen = 0; while (isdigit((unsigned char)*c)) opLen = 10*opLen + (*c++ - '0'); if (opLen == 0) { warn("%s:%d: CIGAR operator length is zero", fileName, lineIx); return FALSE; } op = *c++; switch (op) { case 'M': case 'X': case '=': qPos += opLen; tPos += opLen; lens += opLen; break; case 'I': if (prevOp == '\0') // leading insertion insl = opLen; else { pushBlock(psl, blockSpace, qPos-lens, tPos-lens, lens); lens = 0; } qNumInsert += 1; qBaseInsert += opLen; qPos += opLen; break; case 'D': if (prevOp == '\0') // leading deletion insl = -opLen; else { pushBlock(psl, blockSpace, qPos-lens, tPos-lens, lens); lens = 0; } tNumInsert += 1; tBaseInsert += opLen; tPos += opLen; break; default: warn("%s:%d: invalid CIGAR operator '%c'", fileName, lineIx, op); return FALSE; } prevOp = op; } // the last CIGAR operator if (prevOp == 'I') // trailing insertion insr = opLen; else if (prevOp == 'D') // trailing deletion insr = -opLen; else pushBlock(psl, blockSpace, qPos-lens, tPos-lens, lens); if (qPos != psl->qEnd - psl->qStart) { warn("%s:%d: CIGAR length does not match alignment length (query): %d != %d", fileName, lineIx, psl->qEnd - psl->qStart, qPos); return FALSE; } if (tPos != psl->tEnd - psl->tStart) { warn("%s:%d: CIGAR length does not match alignment length (target): %d != %d", fileName, lineIx, psl->tEnd - psl->tStart, tPos); return FALSE; } +// block offsets computed above are measured from position 0 of the CIGAR, +// which is the *untrimmed* qStart/tStart the PAF reported -- save those +// before trimming for leading/trailing indels below, so the shift to +// absolute coordinates doesn't double-count the trim. +int origQStart = psl->qStart; +int origQEnd = psl->qEnd; +int origTStart = psl->tStart; + // handle leading and trailing indels: PSL blocks must start and end on a match if (insl > 0) { qNumInsert -= 1; qBaseInsert -= insl; psl->qStart += insl; } else if (insl < 0) { tNumInsert -= 1; tBaseInsert += insl; psl->tStart -= insl; } if (insr > 0) { qNumInsert -= 1; qBaseInsert -= insr; psl->qEnd -= insr; } else if (insr < 0) { tNumInsert -= 1; tBaseInsert += insr; psl->tEnd += insr; } // shift target block positions to absolute target coordinates for (i = 0; i < psl->blockCount; i++) - psl->tStarts[i] += psl->tStart; + psl->tStarts[i] += origTStart; // shift query block positions to absolute coordinates, taking the query // strand into account if (psl->strand[0] == '-') for (i = 0; i < psl->blockCount; i++) - psl->qStarts[i] = psl->qSize - psl->qEnd + psl->qStarts[i]; + psl->qStarts[i] = psl->qSize - origQEnd + psl->qStarts[i]; else for (i = 0; i < psl->blockCount; i++) - psl->qStarts[i] += psl->qStart; + psl->qStarts[i] += origQStart; psl->qNumInsert = qNumInsert; psl->qBaseInsert = qBaseInsert; psl->tNumInsert = tNumInsert; psl->tBaseInsert = tBaseInsert; int misMatch = psl->qEnd - psl->qStart - qBaseInsert - (int)psl->match; if (misMatch < 0) { warn("%s:%d: negative misMatch value: %d", fileName, lineIx, misMatch); return FALSE; } psl->misMatch = misMatch; lens = 0; for (i = 0; i < psl->blockCount; i++) lens += psl->blockSizes[i]; int nCount = lens - (int)psl->match - (int)psl->misMatch - (int)psl->repMatch; if (nCount < 0) { warn("%s:%d: negative nCount value: %d", fileName, lineIx, nCount); return FALSE; } psl->nCount = nCount; return TRUE; } static void pafToPsl(char *inFile, char *outFile) /* pafToPsl - converting paf output from minimap2 into UCSC psl format. */ { struct lineFile *lf = lineFileOpen(inFile, TRUE); FILE *f = mustOpen(outFile, "w"); int tagLen = strlen(cigarTag); struct hash *tSizeHash = tSizesFile ? hashNameIntFile(tSizesFile) : NULL; struct hash *qSizeHash = qSizesFile ? hashNameIntFile(qSizesFile) : NULL; char *line; int lineSize; while (lineFileNext(lf, &line, &lineSize)) { char *s = line; char *fields[11]; int i; for (i = 0; i < ArraySize(fields); i++) { fields[i] = nextWord(&s); if (fields[i] == NULL) break; } if (i < ArraySize(fields)) { warn("%s:%d: PAF line has fewer than %d fields, skipping", lf->fileName, lf->lineIx, (int)ArraySize(fields)); continue; } char *cigar = NULL; char *tag; while ((tag = nextWord(&s)) != NULL) { if ((int)strlen(tag) > tagLen && startsWith(cigarTag, tag)) { cigar = tag + tagLen; break; } } if (cigar == NULL) { warn("%s:%d: PAF line is missing a %s CIGAR tag, skipping", lf->fileName, lf->lineIx, cigarTag); continue; } char strand[2]; strand[0] = fields[4][0]; strand[1] = '\0'; if (strand[0] != '+' && strand[0] != '-') { warn("%s:%d: invalid PAF strand '%c', skipping", lf->fileName, lf->lineIx, strand[0]); continue; } unsigned qSize = sqlUnsigned(fields[1]); if (qSizeHash != NULL) { int sizesVal = hashIntValDefault(qSizeHash, fields[0], -1); if (sizesVal < 0) { warn("%s:%d: query '%s' not found in %s, skipping", lf->fileName, lf->lineIx, fields[0], qSizesFile); continue; } if ((unsigned)sizesVal != qSize) warn("%s:%d: query '%s' size %u in PAF does not match %d in %s, using %s", lf->fileName, lf->lineIx, fields[0], qSize, sizesVal, qSizesFile, qSizesFile); qSize = (unsigned)sizesVal; } unsigned tSize = sqlUnsigned(fields[6]); if (tSizeHash != NULL) { int sizesVal = hashIntValDefault(tSizeHash, fields[5], -1); if (sizesVal < 0) { warn("%s:%d: target '%s' not found in %s, skipping", lf->fileName, lf->lineIx, fields[5], tSizesFile); continue; } if ((unsigned)sizesVal != tSize) warn("%s:%d: target '%s' size %u in PAF does not match %d in %s, using %s", lf->fileName, lf->lineIx, fields[5], tSize, sizesVal, tSizesFile, tSizesFile); tSize = (unsigned)sizesVal; } int blockSpace = 16; struct psl *psl = pslNew(fields[0], qSize, sqlSigned(fields[2]), sqlSigned(fields[3]), fields[5], tSize, sqlSigned(fields[7]), sqlSigned(fields[8]), strand, blockSpace, 0); psl->match = sqlUnsigned(fields[9]); // fields[10], the PAF "number of minimizers"/alignment block length // field, is not used -- as in the original converter. if (cigarToPsl(psl, &blockSpace, cigar, lf->fileName, lf->lineIx)) pslTabOut(psl, f); pslFree(&psl); } carefulClose(&f); lineFileClose(&lf); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 3) usage(); cigarTag = optionVal("cigarTag", cigarTag); if (strlen(cigarTag) != 5 || cigarTag[2] != ':' || cigarTag[4] != ':') errAbort("-cigarTag must look like xx:Z: (got '%s')", cigarTag); tSizesFile = optionVal("tSizes", NULL); qSizesFile = optionVal("qSizes", NULL); pafToPsl(argv[1], argv[2]); return 0; }