787bbf7122c1c5690af479fdd5639464ec7d5875 angie Thu Mar 4 11:26:44 2021 -0800 Show usage message if given -h or --help. Would be nice for optionInit to take a usage function as arg so an errCatch wasn't necessary. diff --git src/hg/utils/faToVcf/faToVcf.c src/hg/utils/faToVcf/faToVcf.c index ed9e691..f947a86 100644 --- src/hg/utils/faToVcf/faToVcf.c +++ src/hg/utils/faToVcf/faToVcf.c @@ -1,392 +1,409 @@ /* faToVcf - Convert a FASTA alignment file to VCF. */ #include "common.h" +#include "errCatch.h" #include "fa.h" #include "linefile.h" #include "hash.h" #include "iupac.h" #include "options.h" -void usage() +void usage(int exitCode) /* Explain usage and exit. */ { -errAbort( +fputs( "faToVcf - Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs\n" "usage:\n" " faToVcf in.fa out.vcf\n" "options:\n" " -ambiguousToN Treat all IUPAC ambiguous bases (N, R, V etc) as N (no call).\n" " -excludeFile=file Exclude sequences named in file which has one sequence name per line\n" " -includeRef Include the reference in the genotype columns\n" " (default: omitted as redundant)\n" " -maskSites=file Exclude variants in positions recommended for masking in file\n" " (typically https://github.com/W-L/ProblematicSites_SARS-CoV2/raw/master/problematic_sites_sarsCov2.vcf)\n" " -minAc=N Ignore alternate alleles observed fewer than N times\n" " -noGenotypes Output 8-column VCF, without the sample genotype columns\n" " -ref=seqName Use seqName as the reference sequence; must be present in faFile\n" " (default: first sequence in faFile)\n" " -resolveAmbiguous For IUPAC ambiguous characters like R (A or G), if the character\n" " represents two bases and one is the reference base, convert it to the\n" " non-reference base. Otherwise convert it to N.\n" " -startOffset=N Add N bases to each position (for trimmed alignments)\n" " -vcfChrom=seqName Use seqName for the CHROM column in VCF (default: ref sequence)\n" "in.fa must contain a series of sequences with different names and the same length.\n" "Both N and - are treated as missing information.\n" + , stderr ); +exit(exitCode); } #define MAX_ALTS 256 /* Command line validation table. */ static struct optionSpec options[] = { { "ambiguousToN", OPTION_BOOLEAN }, { "excludeFile", OPTION_STRING }, { "includeRef", OPTION_BOOLEAN }, { "maskSites", OPTION_STRING }, { "minAc", OPTION_INT }, { "noGenotypes", OPTION_BOOLEAN }, { "ref", OPTION_STRING }, { "resolveAmbiguous", OPTION_BOOLEAN }, { "startOffset", OPTION_INT}, { "vcfChrom", OPTION_STRING }, + { "h", OPTION_BOOLEAN }, + { "-help", OPTION_BOOLEAN }, { NULL, 0 }, }; static struct dnaSeq *removeExcludedSequences(struct dnaSeq *sequences) /* If -excludeFile was passed in, remove any sequences whose names are found in the file and * return the modified list. */ { char *excludeFile = optionVal("excludeFile", NULL); if (excludeFile) { struct lineFile *lf = lineFileOpen(excludeFile, TRUE); struct hash *excludedSeqs = hashNew(0); char *line; while (lineFileNextReal(lf, &line)) { line = trimSpaces(line); hashAdd(excludedSeqs, line, NULL); } lineFileClose(&lf); // Make sure there's not a conflict between the reference sequence and the excluded seqs char *explicitRef = optionVal("ref", NULL); if (explicitRef && hashLookup(excludedSeqs, explicitRef)) errAbort("-ref sequence '%s' is included in -excludeFile %s." "Please resolve this contradiction.", explicitRef, excludeFile); int excludeCount = 0; struct dnaSeq *newList = NULL, *seq, *nextSeq = NULL; for (seq = sequences; seq != NULL; seq = nextSeq) { nextSeq = seq->next; if (hashLookup(excludedSeqs, seq->name)) excludeCount++; else slAddHead(&newList, seq); } hashFree(&excludedSeqs); slReverse(&newList); sequences = newList; verbose(2, "Excluded %d sequences named in %s (%d sequences remaining including reference)\n", excludeCount, excludeFile, slCount(sequences)); } return sequences; } static struct dnaSeq *readSequences(char *faFile) /* Read all sequences in faFile. Make sure there are at least 2 sequences and that * all have the same length. If a reference sequence is specified and is not the first * sequence in the file, then move the reference sequence to the head of the list. */ { verbose(2, "Reading sequences from %s\n", faFile); struct dnaSeq *sequences = faReadAllMixed(faFile); int seqCount = slCount(sequences); verbose(2, "Read %d sequences.\n", seqCount); if (seqCount < 2) errAbort("faToVcf: expecting multiple sequences in %s but found only %d.", faFile, seqCount); int seqSize = sequences->size; struct dnaSeq *seq; for (seq = sequences->next; seq != NULL; seq = seq->next) if (seq->size != seqSize) errAbort("faToVcf: first sequence in %s (%s) has size %d, but sequence %s has size %d. " "All sequences must have the same size.", faFile, sequences->name, seqSize, seq->name, seq->size); char *refName = optionVal("ref", sequences->name); if (differentString(sequences->name, refName)) { verbose(2, "Using %s as reference.\n", refName); struct dnaSeq *seq; for (seq = sequences; seq->next != NULL; seq = seq->next) { if (sameString(seq->next->name, refName)) { struct dnaSeq *ref = seq->next; seq->next = ref->next; ref->next = sequences; sequences = ref; break; } } if (differentString(sequences->name, refName)) errAbort("Could not find -ref sequence '%s' in %s.", refName, faFile); } sequences = removeExcludedSequences(sequences); return sequences; } static void writeVcfHeader(FILE *outF, char *faFile, char *vcfFile, struct dnaSeq *sequences, boolean includeRef, boolean includeGenotypes) /* Write a simple VCF header with sequence names as genotype columns. */ { fprintf(outF, "##fileformat=VCFv4.2\n" "##reference=%s:%s\n" "##source=faToVcf %s %s\n" //#*** Should document options used. "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO", faFile, sequences->name, faFile, vcfFile); if (includeGenotypes) { fprintf(outF, "\tFORMAT"); struct dnaSeq *seqsForGt = (includeRef ? sequences : sequences->next), *seq; for (seq = seqsForGt; seq != NULL; seq = seq->next) fprintf(outF, "\t%s", seq->name); } fprintf(outF, "\n"); } static boolean *getMaskSites(char *maskSitesFile, struct dnaSeq *ref) /* If -maskSites=file is given, parse sites to be masked from file (expecting VCF with 'mask' in * the filter column at reference positions to be masked) and return an array of booleans indexed * by reference position, TRUE for mask. Otherwise return NULL. */ { boolean *maskSites = NULL; if (maskSitesFile) { int chromSize = strlen(ref->dna) - countChars(ref->dna, '-'); AllocArray(maskSites, chromSize); struct lineFile *lf = lineFileOpen(maskSitesFile, TRUE); char *line; while (lineFileNext(lf, &line, NULL)) { if (line[0] == '#') continue; char *words[9]; int wordCount = chopTabs(line, words); lineFileExpectWords(lf, 8, wordCount); if (!isAllDigits(words[1])) lineFileAbort(lf, "Expected second column to contain numeric position but got '%s'", words[1]); int pos = atol(words[1]); if (pos < 1 || pos > chromSize) { warn("Warning line %d of %s: " "Expected second column to contain positions between 1 and %d but got %d", lf->lineIx, lf->fileName, chromSize, pos); } else if (sameString(words[6], "mask")) maskSites[pos-1] = TRUE; } lineFileClose(&lf); } return maskSites; } void faToVcf(char *faFile, char *vcfFile) /* faToVcf - Convert a FASTA alignment file to VCF. */ { struct dnaSeq *sequences = readSequences(faFile); int seqCount = slCount(sequences); int seqSize = sequences->size; boolean includeRef = optionExists("includeRef"); verbose(2, "Writing VCF to %s\n", vcfFile); FILE *outF = mustOpen(vcfFile, "w"); boolean noGenotypes = optionExists("noGenotypes"); writeVcfHeader(outF, faFile, vcfFile, sequences, includeRef, !noGenotypes); struct dnaSeq *refSeq = sequences; char *vcfChrom = optionVal("vcfChrom", refSeq->name); int startOffset = optionInt("startOffset", 0); boolean *maskSites = getMaskSites(optionVal("maskSites", NULL), refSeq); struct dnaSeq *seqsForGt = (includeRef ? sequences : sequences->next); int gtCount = includeRef ? seqCount : seqCount - 1; int *genotypes = needMem(sizeof(int) * gtCount); boolean *missing = needMem(sizeof(boolean) * gtCount); int baseIx, chromStart = 0; for (baseIx = 0, chromStart = 0; baseIx < seqSize; baseIx++, chromStart++) { char ref = toupper(refSeq->dna[baseIx]); if (ref == '-') { // Insertion into reference -- ignore and adjust reference coordinate. chromStart--; continue; } if (ref == 'N') continue; if (maskSites && maskSites[chromStart]) continue; if (ref == 'U') ref = 'T'; char altAlleles[MAX_ALTS]; int altAlleleCounts[MAX_ALTS]; int altCount = 0; memset(altAlleles, 0, sizeof(altAlleles)); memset(genotypes, 0, sizeof(int) * gtCount); memset(missing, 0, sizeof(boolean) * gtCount); int nonNCount = seqCount; struct dnaSeq *seq; int gtIx; for (seq = seqsForGt, gtIx = 0; seq != NULL; seq = seq->next, gtIx++) { char al = toupper(seq->dna[baseIx]); if (al == 'U') al = 'T'; if (isIupacAmbiguous(al)) { if (optionExists("ambiguousToN")) al = 'N'; else if (optionExists("resolveAmbiguous")) { char *bases = iupacAmbiguousToString(al); if (strlen(bases) > 2 || (toupper(bases[0]) != ref && toupper(bases[1]) != ref)) al = 'N'; else if (toupper(bases[0]) == ref) al = toupper(bases[1]); else al = toupper(bases[0]); } } if (al == 'N' || al == '-') { missing[gtIx] = TRUE; nonNCount--; } else if (al != ref) { char *altFound = strchr(altAlleles, al); int altIx = 0; if (! altFound) { altIx = altCount++; if (altCount == MAX_ALTS) errAbort("faToVcf: fasta base %d (reference base %d) has at least %d alternate alleles; increase " "MAX_ALTS in faToVcf.c!", baseIx, chromStart, MAX_ALTS); altAlleleCounts[altIx] = 1; altAlleles[altIx] = al; } else { altIx = altFound - altAlleles; altAlleleCounts[altIx]++; } genotypes[gtIx] = altIx+1; } } int minAc = optionInt("minAc", 0); if (minAc > 0) { int oldToNewIx[altCount]; char newAltAlleles[altCount]; int newAltAlleleCounts[altCount]; int newAltCount = 0; int altIx; for (altIx = 0; altIx < altCount; altIx++) { if (altAlleleCounts[altIx] >= minAc) { // This alt passes the filter. int newAltIx = newAltCount++; newAltAlleleCounts[newAltIx] = altAlleleCounts[altIx]; newAltAlleles[newAltIx] = altAlleles[altIx]; oldToNewIx[altIx] = newAltIx; } else { // We're removing this alt; count its genotypes as missing since they're not // really reference. for (gtIx = 0; gtIx < gtCount; gtIx++) if (genotypes[gtIx] == altIx+1) { missing[gtIx] = TRUE; nonNCount--; } oldToNewIx[altIx] = -1; } } if (newAltCount != altCount) { for (gtIx = 0; gtIx < gtCount; gtIx++) { int oldGt = genotypes[gtIx]; if (oldGt == 0) genotypes[gtIx] = 0; else genotypes[gtIx] = oldToNewIx[oldGt-1] + 1; } altCount = newAltCount; for (altIx = 0; altIx < newAltCount; altIx++) { altAlleles[altIx] = newAltAlleles[altIx]; altAlleleCounts[altIx] = newAltAlleleCounts[altIx]; } } } if (altCount) { int pos = chromStart + startOffset + 1; fprintf(outF, "%s\t%d\t", vcfChrom, pos); int altIx; for (altIx = 0; altIx < altCount; altIx++) fprintf(outF, "%s%c%d%c", (altIx > 0) ? "," : "", ref, pos, altAlleles[altIx]); fprintf(outF, "\t%c\t", ref); for (altIx = 0; altIx < altCount; altIx++) { if (altIx > 0) fprintf(outF, ","); fprintf(outF, "%c", altAlleles[altIx]); } fprintf(outF, "\t.\t.\tAC="); for (altIx = 0; altIx < altCount; altIx++) { if (altIx > 0) fprintf(outF, ","); fprintf(outF, "%d", altAlleleCounts[altIx]); } fprintf(outF, ";AN=%d", nonNCount); if (!noGenotypes) { fputs("\tGT", outF); for (gtIx = 0; gtIx < gtCount; gtIx++) { if (missing[gtIx]) fprintf(outF, "\t."); else fprintf(outF, "\t%d", genotypes[gtIx]); } } fprintf(outF, "\n"); } } carefulClose(&outF); } int main(int argc, char *argv[]) /* Process command line. */ { +struct errCatch *errCatch = errCatchNew(); +if (errCatchStart(errCatch)) optionInit(&argc, argv, options); +errCatchEnd(errCatch); +if (errCatch->gotError) + { + warn("%s", errCatch->message->string); + usage(1); + } +errCatchFree(&errCatch); + if (optionExists("ambiguousToN") && optionExists("resolveAmbiguous")) errAbort("-ambiguousToN and -resolveAmbiguous conflict with each other; " "please use only one."); +if (optionExists("h") || optionExists("-help")) + usage(0); if (argc != 3) - usage(); + usage(1); faToVcf(argv[1], argv[2]); return 0; }