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/encode/regionAgp/regionAgp.c src/hg/encode/regionAgp/regionAgp.c index bdec193..d2823a1 100644 --- src/hg/encode/regionAgp/regionAgp.c +++ src/hg/encode/regionAgp/regionAgp.c @@ -1,230 +1,230 @@ /* regionAgp - generate an AGP file for an ENCODE region described in * a bed file, containing lines of the format: * <chrom> <start> <end> <region> * based on the chromosome AGP's. */ /* 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 "options.h" #include "bed.h" #include "agp.h" #include "agpFrag.h" #include "agpGap.h" #include "contigAcc.h" #define DIR_OPTION "dir" #define NAME_PREFIX_OPTION "namePrefix" #define CONTIG_FILE_OPTION "contigFile" static struct optionSpec options[] = { {DIR_OPTION, OPTION_BOOLEAN}, {NAME_PREFIX_OPTION, OPTION_STRING}, {CONTIG_FILE_OPTION, OPTION_STRING}, {NULL, 0} }; bool dirOption = FALSE; char *namePrefix = ""; char *contigFile = NULL; void usage() /* Print usage instructions and exit. */ { errAbort( "regionAgp - generate an AGP file for a region\n\n\ usage:\n\ regionAgp region.bed chrom.agp out\n\ region.bed describes the region with lines formatted:\n\ <chrom> <start> <end> <region> <seq no>\n\ chrom.agp is the input AGP file\n\ out is the output AGP file, or directory if -dir option used\n\ options:\n\ -%s prefix for sequence name and AGP file (usually species_)\n\ -%s file name for contig/accession map (dump of contigAcc table).\n\ Used if AGP contains unaccessioned contigs.\n\ -%s directory for output AGP files, to be named <region>.agp", NAME_PREFIX_OPTION, CONTIG_FILE_OPTION, DIR_OPTION); } struct hash *contigAccLoadToHash(char *contigFile) /* load accessions into hash by contig name */ { struct hash *contigAccHash = newHash(0); struct contigAcc *contigAcc, *contigAccList; contigAccList = contigAccLoadAll(contigFile); if (contigAccList == NULL) return NULL; for (contigAcc = contigAccList; contigAcc->next; contigAcc = contigAcc->next) hashAddUnique(contigAccHash, contigAcc->contig, contigAcc->acc); return contigAccHash; } void regionAgp(char *bedFile, char *agpIn, char *agpOut) /* regionAgp - generate an AGP file for a region described in a bed file, * based on a chromosome-based AGP */ { struct bed *pos, *posList; struct hash *agpHash; struct agp *agpList, *agp; FILE *fout = NULL; int start = 1; int seqNum = 1; char regionName[64]; char outFile[64]; struct contigAcc *contigAcc, *contigAccList; struct hash *contigAccHash = NULL; /* read in BED file with chromosome coordinate ranges */ fprintf(stderr, "Loading bed file...\n"); posList = bedLoadNAll(bedFile, 5); /* read chrom AGP file into a hash of AGP's, one per chrom */ fprintf(stderr, "Loading AGP's...\n"); agpHash = agpLoadAll(agpIn); fprintf(stderr, "Creating new AGP's...\n"); if (!dirOption) fout = mustOpen(agpOut, "w"); if (contigFile != NULL) { /* read in contig to accession mapping */ contigAccHash = contigAccLoadToHash(contigFile); if (contigAccHash == NULL) errAbort("Empty contig file: %s", contigFile); } /* process BED lines, emitting an AGP file */ for (pos = posList; pos != NULL; pos = pos->next) { /* convert BED start to 1-based, since AGP is */ pos->chromStart++; if (pos->score == 1) /* score field of the BED is actually the sequence number * of the segment in the region */ start = 1; verbose(2, "chr=%s, start=%d, end=%d, region=%s, seqnum=%d\n", pos->chrom, pos->chromStart, pos->chromEnd, pos->name, pos->score); safef(regionName, ArraySize(regionName), "%s%s_%d", namePrefix, pos->name, pos->score); if (dirOption) { start = 1; seqNum = 1; safef(outFile, ArraySize(outFile), "%s/%s.agp", agpOut, regionName); fout = mustOpen(outFile, "w"); } agpList = (struct agp *)hashMustFindVal(agpHash, pos->chrom); for (agp = agpList; agp != NULL; agp = agp->next) { if (agp->isFrag) { /* fragment */ int chromStart, chromEnd; struct agpFrag frag, *agpFrag = (struct agpFrag *)agp->entry; int offset = 0, fragLen = 0; /* determine if this AGP entry intersects the range */ if (pos->chromEnd < agpFrag->chromStart || pos->chromStart > agpFrag->chromEnd) continue; chromStart = max(pos->chromStart, agpFrag->chromStart); chromEnd = min(pos->chromEnd, agpFrag->chromEnd); fragLen = chromEnd - chromStart + 1; /* populate the fragment */ frag.chrom = regionName; frag.chromStart = start - 1; // agpFragOutput adds 1 frag.chromEnd = frag.chromStart + fragLen; verbose(3, "pos start=%d, agp start = %d\n", pos->chromStart, agpFrag->chromStart); offset = pos->chromStart - agpFrag->chromStart; offset = max(0, offset); verbose(3, "offset=%d\n", offset); if (agpFrag->strand[0] == '-') { frag.fragEnd = agpFrag->fragEnd - offset; frag.fragStart = frag.fragEnd - fragLen; verbose(3, "fragStart = %d, fragEnd = %d\n", frag.fragStart, frag.fragEnd); } else { frag.fragStart = agpFrag->fragStart + offset - 1; frag.fragEnd = frag.fragStart + fragLen; } start = frag.chromEnd + 1; frag.ix = seqNum++;; frag.type[0] = agpFrag->type[0]; frag.type[1] = 0; if (contigFile) frag.frag = hashMustFindVal(contigAccHash, agpFrag->frag); else frag.frag = agpFrag->frag; frag.strand[0] = agpFrag->strand[0]; /* NCBI AGP format requires strand to be + or - (internally we sometimes use '.' to indicate we don't know) */ if (frag.strand[0] == '.') frag.strand[0] = '+'; frag.strand[1] = 0; agpFragOutput(&frag, fout, '\t', '\n'); } else { /* gap */ struct agpGap gap, *agpGap = (struct agpGap *)agp->entry; int chromEnd = agpGap->chromStart + agpGap->size - 1; /* determine if this AGP entry intersects the range */ if (pos->chromEnd < agpGap->chromStart || pos->chromStart > agpGap->chromEnd) continue; gap.chrom = regionName; gap.chromStart = start; gap.chromEnd = gap.chromStart + agpGap->size - 1; start = gap.chromEnd + 1; gap.ix = seqNum++;; gap.n[0] = 'N'; gap.n[1] = 0; gap.size = agpGap->size; gap.type = agpGap->type; gap.bridge = agpGap->bridge; agpGapOutput(&gap, fout, '\t', '\n'); } } if (dirOption) carefulClose(&fout); } if (!dirOption) carefulClose(&fout); } int main(int argc, char *argv[]) /* Process command line. */ { char *regionBedFile; char *chromAgpFile; char *out; optionInit(&argc, argv, options); dirOption = optionExists(DIR_OPTION); namePrefix = optionVal(NAME_PREFIX_OPTION, ""); contigFile = optionVal(CONTIG_FILE_OPTION, NULL); if (argc != 4) usage(); regionBedFile = argv[1]; chromAgpFile = argv[2]; out = argv[3]; regionAgp(regionBedFile, chromAgpFile, out); return 0; }