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/ratStuff/mafSplitPos/mafSplitPos.c src/hg/ratStuff/mafSplitPos/mafSplitPos.c index a2db948..07c579c 100644 --- src/hg/ratStuff/mafSplitPos/mafSplitPos.c +++ src/hg/ratStuff/mafSplitPos/mafSplitPos.c @@ -1,199 +1,199 @@ /* Determine best positions to split input to * a multiple alignment -- places where the MAF * is likely to split; e.g. at gaps in the reference. * For use with "mafSplit" */ /* Copyright (C) 2013 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 "obscure.h" #include "options.h" #include "jksql.h" #include "sqlNum.h" #include "hdb.h" void usage() /* Explain usage and exit. */ { errAbort( "mafSplitPos - Pick positions to split multiple alignment input files\n" "usage:\n" " mafSplitPos database size(Mbp) out.bed\n" "options:\n" " -chrom=chrN Restrict to one chromosome\n" " -minGap=N Split only on gaps >N bp, defaults to 100, specify -1 to disable\n" " -minRepeat=N Split only on repeats >N bp, defaults to 100, specify -1 to disable\n" ); } static struct optionSpec options[] = { {"chrom", OPTION_STRING}, {"minGap", OPTION_INT}, {"minRepeat", OPTION_INT}, {NULL, 0}, }; static char *chrom = NULL; static int minGap = 100; static int minRepeat = 100; static char *db = NULL; int nextGapPos(char *chrom, int desiredPos, struct sqlConnection *conn) { /* Find next gap on the chrom and return midpoint */ struct sqlResult *sr; char **row; int pos = -1; int start, end; struct hTableInfo *hti = hFindTableInfo(db, chrom, "gap"); struct dyString *query = newDyString(1024); if (hti == NULL) errAbort("table %s.gap doesn't exist", db); sqlDyStringPrintf(query, "select chromStart,chromEnd from "); if (hti->isSplit) dyStringPrintf(query, "%s_gap where ", chrom); else dyStringPrintf(query, "gap where %s='%s' AND ", hti->chromField, chrom); dyStringPrintf(query, "(chromStart >= %d and chromEnd-chromStart > %d)\ order by chromStart limit 1", desiredPos, minGap); sr = sqlGetResult(conn, query->string); freeDyString(&query); if ((row = sqlNextRow(sr)) != NULL) { start = sqlSigned(row[0]); end = sqlSigned(row[1]); pos = start + (end - start)/2; } sqlFreeResult(&sr); return pos; } int nextRepeatPos(char *chrom, int desiredPos, struct sqlConnection *conn) /* Find next 0% diverged repeat on the chrom and return midpoint */ { struct sqlResult *sr; char **row; int pos = -1; int start, end; struct hTableInfo *hti = hFindTableInfo(db, chrom, "rmsk"); struct dyString *query = newDyString(1024); if (hti == NULL) errAbort("table %s.rmsk doesn't exist", db); sqlDyStringPrintf(query, "select genoStart,genoEnd from "); if (hti->isSplit) dyStringPrintf(query, "%s_rmsk where ", chrom); else dyStringPrintf(query, "rmsk where %s='%s' AND ", hti->chromField, chrom); dyStringPrintf(query, "(genoStart >= %d AND \ milliDiv=0 AND \ repClass<>'Simple_repeat' AND repClass<>'Low_complexity' AND \ genoEnd-genoStart>%d) order by genoStart limit 1", desiredPos, minRepeat); sr = sqlGetResult(conn, query->string); freeDyString(&query); if ((row = sqlNextRow(sr)) != NULL) { start = sqlSigned(row[0]); end = sqlSigned(row[1]); pos = start + (end - start)/2; } sqlFreeResult(&sr); return pos; } void chromSplits(char *chrom, int chromSize, int splitSize, struct sqlConnection *conn, FILE *f) /* determine positions on a single chromosome */ { int desiredPos = splitSize; int splitPos = -1; int gapPos = -1; int prevPos = 0; while (desiredPos < chromSize) { splitPos = gapPos = (minGap < 0) ? -1 : nextGapPos(chrom, desiredPos, conn); if (splitPos < 0 || splitPos > desiredPos + (desiredPos/10)) { /* next gap is further out than 10% of desired position, * so look for the next new repeat */ splitPos = (minRepeat < 0) ? -1 : nextRepeatPos(chrom, desiredPos, conn); if (splitPos < 0) splitPos = gapPos; /* no acceptable repeat position */ else if ((gapPos >= 0) && (splitPos > desiredPos)) splitPos = min(splitPos, gapPos); } if (splitPos < 0) /* no places to split on this chrom */ return; fprintf(f, "%s\t%d\t%d\n", chrom, splitPos, splitPos+1), verbose(2, " %s\t%d\n", splitPos == gapPos ? "gap" : "repeat", (splitPos - prevPos)/1000000); prevPos = splitPos; desiredPos = splitPos + splitSize; } } void mafSplitPos(char *database, char *size, char *outFile) /* Pick best positions for split close to size. * Use middle of a gap as preferred site. * If not gaps are in range, use recent repeats (0% diverged) */ { int splitSize = 0; int chromSize = 0; struct hash *chromHash; struct hashCookie hc; struct hashEl *hel; struct sqlConnection *conn = sqlConnect(database); FILE *f; db = database; verbose(1, "Finding split positions for %s at ~%s Mbp intervals\n", database, size); splitSize = sqlSigned(size) * 1000000; if (chrom == NULL) { chromHash = hChromSizeHash(database); } else { chromHash = hashNew(6); hashAddInt(chromHash, chrom, hChromSize(database, chrom)); } conn = sqlConnect(database); f = mustOpen(outFile, "w"); hc = hashFirst(chromHash); while ((hel = hashNext(&hc)) != NULL) { chrom = hel->name; chromSize = ptToInt(hel->val); chromSplits(chrom, chromSize, splitSize, conn, f); } sqlDisconnect(&conn); carefulClose(&f); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); chrom = optionVal("chrom", NULL); minGap = optionInt("minGap", minGap); minRepeat = optionInt("minRepeat", minRepeat); if (argc != 4) usage(); mafSplitPos(argv[1], argv[2], argv[3]); return 0; }