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/utils/scaffoldFaToAgp/scaffoldFaToAgp.c src/hg/utils/scaffoldFaToAgp/scaffoldFaToAgp.c index e2ca8e4..76691c7 100644 --- src/hg/utils/scaffoldFaToAgp/scaffoldFaToAgp.c +++ src/hg/utils/scaffoldFaToAgp/scaffoldFaToAgp.c @@ -1,213 +1,213 @@ /* 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. */ /* scaffoldFaToAgp - read a file containing FA scaffold records and generate */ /* an AGP file, gap file and a lift file */ /* This utility is used when working with genomes that consist * of scaffolds with no chromosome mapping (e.g. Fugu). * The AGP file contains scaffolds and inter-scaffold gaps. * This file is used to generate the assembly ("gold") track. * The "gap" file contains gaps within scaffolds as well * as inter-scaffold gaps. This file is used to generate the "gap" track. * It is formatted similarly to an AGP, but only contains gap entries. * The lift file is associated with the AGP file. It is used to * lift scaffold coordinates to chromosome coordinates. */ #include "common.h" #include "fa.h" #include "options.h" #include "../../hg/inc/agpFrag.h" #include "../../hg/inc/agpGap.h" #define SCAFFOLD_GAP_TYPE "contig" #define FRAGMENT_GAP_TYPE "frag" /* within scaffolds (bridged) */ #define CHROM_NAME "chrUn" int minGapSize = 5; int scaffoldGapSize = 1000; void usage() /* Print usage instructions and exit. */ { errAbort("scaffoldFaToAgp - generate an AGP file, gap file, and lift file from a scaffold FA file.\n" "usage:\n" " scaffoldFaToAgp source.fa\n" "options:\n" " -minGapSize Minimum threshold for calling a block of Ns a gap.\n" " -scaffoldGapSize Size of gaps of Ns to be inserted between scaffolds.\n" "The resulting files will be source.{agp,gap,lft}\n" "Note: unless otherwise specified, gaps of 1000 bases are inserted \n" "between scaffold records by default as contig gaps in the .agp file.\n" " N's within scaffolds are represented as\n" " frag gaps in the .gap file only\n"); } boolean seqGetGap(DNA *seq, int *retSize, int *retGapSize) /* determine size of ungapped sequence, and size of gap following it */ { int seqSize = 0, gapSize = 0; for (; *seq && (*seq != 'n' && *seq != 'N'); seq++, seqSize++); if (retSize) *retSize = seqSize; for (; *seq && (*seq == 'n' || *seq == 'N'); seq++, gapSize++); if (retGapSize) *retGapSize = gapSize; return (seqSize ? TRUE : FALSE); } void scaffoldFaToAgp(char *scaffoldFile) /* scaffoldFaToAgp - create AGP file, gap file and lift file * from scaffold FA file */ { DNA *scaffoldSeq; char *name; int size; struct agpFrag frag; struct agpGap scaffoldGap, fragGap; struct lineFile *lf = lineFileOpen(scaffoldFile, TRUE); char outDir[256], outFile[128], ext[64], outPath[512]; FILE *agpFile = NULL, *gapFile = NULL, *liftFile = NULL; int fileNumber = 1; /* sequence number in AGP file */ int start = 0, end = 0; int chromSize = 0; int scaffoldCount = 0; int fragSize = 0, gapSize = 0; char *seq; int seqStart = 0; /* determine size of "unordered chromosome" that will be constructed. * This is needed for the lift file. */ while (faMixedSpeedReadNext(lf, &scaffoldSeq, &size, &name)) { chromSize += size; chromSize += scaffoldGapSize; scaffoldCount++; } /* do not need the final useless gap */ chromSize -= scaffoldGapSize; printf("scaffold gap size is %d, total scaffolds: %d\n", scaffoldGapSize, scaffoldCount); printf("chrom size is %d\n", chromSize); /* initialize fixed fields in AGP frag */ ZeroVar(&frag); frag.chrom = CHROM_NAME; frag.type[0] = 'D'; /* draft */ frag.fragStart = 0; /* always start at beginning of scaffold */ frag.strand[0] = '+'; /* initialize fixed fields in scaffold gap */ ZeroVar(&scaffoldGap); scaffoldGap.chrom = CHROM_NAME; scaffoldGap.n[0] = 'N'; scaffoldGap.size = scaffoldGapSize; scaffoldGap.type = SCAFFOLD_GAP_TYPE; scaffoldGap.bridge = "no"; /* initialize fixed fields in frag gap */ ZeroVar(&fragGap); fragGap.chrom = CHROM_NAME; fragGap.n[0] = 'N'; fragGap.type = FRAGMENT_GAP_TYPE; fragGap.bridge = "yes"; /* munge file paths */ splitPath(scaffoldFile, outDir, outFile, ext); sprintf(outPath, "%s%s.agp", outDir, outFile); agpFile = mustOpen(outPath, "w"); printf("writing %s\n", outPath); sprintf(outPath, "%s%s.gap", outDir, outFile); gapFile = mustOpen(outPath, "w"); printf("writing %s\n", outPath); sprintf(outPath, "%s%s.lft", outDir, outFile); liftFile = mustOpen(outPath, "w"); printf("writing %s\n", outPath); /* read in scaffolds from fasta file, and generate * the three files */ lineFileSeek(lf, 0, SEEK_SET); boolean allDone = FALSE; allDone = ! faMixedSpeedReadNext(lf, &scaffoldSeq, &size, &name); while (! allDone) { end = start + size; /* setup AGP frag for the scaffold and write to AGP file */ frag.frag = name; frag.ix = fileNumber++; frag.chromStart = start; frag.chromEnd = end; frag.fragEnd = size; agpFragOutput(&frag, agpFile, '\t', '\n'); /* write lift file entry for this scaffold */ fprintf(liftFile, "%d\t%s\t%d\t%s\t%d\n", start, name, size, CHROM_NAME, chromSize); /* write gap file entries for this scaffold */ seq = scaffoldSeq; seqStart = start; while (seqGetGap(seq, &fragSize, &gapSize)) { if (gapSize > minGapSize) { fragGap.size = gapSize; fragGap.chromStart = seqStart + fragSize + 1; fragGap.chromEnd = fragGap.chromStart + gapSize - 1; agpGapOutput(&fragGap, gapFile, '\t', '\n'); } seqStart = seqStart + fragSize + gapSize; seq = seq + fragSize + gapSize; } /* setup AGP gap to separate scaffolds and write to AGP and gap files */ /* Note: may want to suppress final gap -- not needed as separator */ start = end + 1; end = start + scaffoldGapSize - 1; /* Avoid an extra gap on the end - not needed */ allDone = ! faMixedSpeedReadNext(lf, &scaffoldSeq, &size, &name); if (allDone) break; scaffoldGap.ix = fileNumber++; scaffoldGap.chromStart = start; scaffoldGap.chromEnd = end; agpGapOutput(&scaffoldGap, agpFile, '\t', '\n'); agpGapOutput(&scaffoldGap, gapFile, '\t', '\n'); /* write lift file entry for this gap */ fprintf(liftFile, "%d\t%s\t%d\t%s\t%d\n", start-1, "gap", scaffoldGapSize, CHROM_NAME, chromSize); start = end; //freeMem(seq); } carefulClose(&agpFile); carefulClose(&liftFile); carefulClose(&gapFile); lineFileClose(&lf); } int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); minGapSize = optionInt("minGapSize", minGapSize); scaffoldGapSize = optionInt("scaffoldGapSize", scaffoldGapSize); if (argc != 2) usage(); scaffoldFaToAgp(argv[1]); return 0; }