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/makeDb/hgLoadMaf/hgLoadMaf.c src/hg/makeDb/hgLoadMaf/hgLoadMaf.c index 5c0d5cd..c16cf7a 100644 --- src/hg/makeDb/hgLoadMaf/hgLoadMaf.c +++ src/hg/makeDb/hgLoadMaf/hgLoadMaf.c @@ -1,331 +1,331 @@ /* hgLoadMaf - Load a maf file index into the database. */ /* 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 "cheapcgi.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "hdb.h" #include "hgRelate.h" #include "portable.h" #include "maf.h" #include "scoredRef.h" #include "dystring.h" #include "errCatch.h" /* Command line options */ /* multiz currently will generate some alignments that have a missing score * and/or contain only 1 or 2 sequences. Webb Miller recommends these * be ignored, and he intends to remove them from multiz output. * When/if this happens, the -warn option should not be used. */ /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"warn", OPTION_BOOLEAN}, {"WARN", OPTION_BOOLEAN}, {"test", OPTION_STRING}, {"pathPrefix", OPTION_STRING}, {"loadFile", OPTION_STRING}, {"tmpDir", OPTION_STRING}, {"refDb", OPTION_STRING}, {"maxNameLen", OPTION_INT}, {"defPos", OPTION_STRING}, {"custom", OPTION_BOOLEAN}, {NULL, 0} }; boolean warnOption = FALSE; boolean warnVerboseOption = FALSE; /* print warning detail */ char *testFile = NULL; /* maf filename if testing */ char *pathPrefix = NULL; /* extFile directory */ static char *tmpDir = NULL; /* location to create a temporary file */ char *loadFile; /* file to read maf file from */ char *refDb; /* reference db (for custom tracks) */ int maxNameLen = 0; /* maximum chrom name length */ char *defPosFile; /* file to put default pos in */ boolean isCustom; /* we're loading a custom track */ void usage() /* Explain usage and exit. */ { errAbort( "hgLoadMaf - Load a maf file index into the database\n" "usage:\n" " hgLoadMaf database table\n" "options:\n" " -warn warn instead of error upon empty/incomplete alignments\n" " -WARN warn instead of error, with detail for the warning\n" " -test=infile use infile as input, and suppress loading\n" " the database. Just create .tab file in current dir.\n" " -pathPrefix=dir load files from specified directory \n" " (default /gbdb/database/table.\n" " -tmpDir=<path> path to directory for creation of temporary .tab file\n" " which will be removed after loading\n" " -loadFile=file use file as input\n" " -maxNameLen=N specify max chromosome name length to avoid\n" " reference to chromInfo table\n" " -defPos=file file to put default position in\n" " default position is first block\n" " -custom loading a custom track, don't use history\n" " or extFile tables\n" "\n" "NOTE: The maf files need to be in chromosome coordinates,\n" " the reference species must be the first component, and \n" " the blocks must be correctly ordered and be on the\n" " '+' strand\n" ); } struct mafComp *findComponent(struct mafAli *maf, char *prefix) /* Find maf component with the given prefix. */ { int preLen = strlen(prefix); struct mafComp *mc; for (mc = maf->components; mc != NULL; mc = mc->next) { if (memcmp(mc->src, prefix, preLen) == 0 && mc->src[preLen] == '.') return mc; } return NULL; } void hgLoadMaf(char *database, char *table) /* hgLoadMaf - Load a maf file index into the database. */ { struct fileInfo *fileList = NULL, *fileEl; struct sqlConnection *conn; long mafCount = 0; FILE *f = NULL; char extFileDir[512]; char ext[10]; char file[100]; int indexLen; if (refDb == NULL) refDb = database; if (tmpDir == NULL) f = hgCreateTabFile(".", table); else f = hgCreateTabFile(tmpDir, table); if (testFile != NULL) { if (!fileExists(testFile)) errAbort("Test file %s doesn't exist\n", testFile); splitPath(testFile, extFileDir, file, ext); strcat(file, ext); fileList = listDirX(extFileDir, file, TRUE); pathPrefix = extFileDir; } else { if (maxNameLen) indexLen = maxNameLen; else indexLen = hGetMinIndexLength(database); if (loadFile != NULL) { if (!fileExists(loadFile)) errAbort("Load file %s doesn't exist\n", loadFile); splitPath(loadFile, extFileDir, file, ext); strcat(file, ext); pathPrefix = extFileDir; fileList = listDirX(pathPrefix, file, TRUE); if (fileList == NULL) fileList = listDirX(".", file, TRUE); } else { if (pathPrefix == NULL) { safef(extFileDir, sizeof(extFileDir), "/gbdb/%s/%s", database, table); pathPrefix = extFileDir; } fileList = listDirX(pathPrefix, "*.maf", TRUE); } if (isCustom) conn = sqlConnect(database); else conn = hgStartUpdate(database); scoredRefTableCreate(conn, table, indexLen); } if (fileList == NULL) errAbort("%s doesn't exist or doesn't have any maf files", pathPrefix); for (fileEl = fileList; fileEl != NULL; fileEl = fileEl->next) { char *fileName = fileEl->name; struct mafFile *mf; struct mafComp *mc; struct scoredRef mr; struct mafAli *maf; off_t offset; int warnCount = 0; int dbNameLen = strlen(refDb); HGID extId; if ((testFile != NULL) || isCustom) extId = 0; else extId = hgAddToExtFile(fileName, conn); struct errCatch *errCatch = errCatchNew(); char *errMsg = NULL; if (errCatchStart(errCatch)) { mf = mafOpen(fileName); verbose(1,"Indexing and tabulating %s\n", fileName); while ((maf = mafNextWithPos(mf, &offset)) != NULL) { double maxScore, minScore; mc = findComponent(maf, refDb); if (mc == NULL) { char msg[2048]; safef(msg, sizeof(msg), "Couldn't find %s. sequence line %d of %s\n", refDb, mf->lf->lineIx, fileName); if (warnOption || warnVerboseOption) { warnCount++; if (warnVerboseOption) verbose(1, "%s", msg); mafAliFree(&maf); continue; } else errAbort("%s", msg); } ZeroVar(&mr); mr.chrom = mc->src + dbNameLen + 1; mr.chromStart = mc->start; mr.chromEnd = mc->start + mc->size; if (mc->strand == '-') reverseUnsignedRange(&mr.chromStart, &mr.chromEnd, mc->srcSize); mr.extFile = extId; mr.offset = offset; if (defPosFile != NULL) { FILE *f = mustOpen(defPosFile, "w"); fprintf(f, "%s:%d-%d\n",mr.chrom, mr.chromStart+1, mr.chromEnd); fclose(f); defPosFile = NULL; } /* The maf scores are the sum of all pairwise * alignment scores. If you have A,B,C,D * species in the alignments it's the sum of * the AB, AC, AD, BC, BD, CD pairwise scores. * If you just had two species it would just * be a single pairwise score. Since we don't * want to penalize things for missing species, * we basically divide by the number of possible * pairings. To get it from the -100 to +100 (more or * less) per base blastz scoring scheme to something * that goes from 0 to 1, we also also divide by 200. * JK */ /* scale using alignment size to get per-base score */ mr.score = maf->score/mc->size; /* get scoring range -- depends on #species in alignment */ mafColMinMaxScore(maf, &minScore, &maxScore); if (maxScore == minScore) /* protect against degenerate case -- 1 species, produces * max & min score of 0 */ mr.score = 0.0; else /* translate to get zero-based score, * then scale by blastz scoring range */ mr.score = (mr.score-minScore)/(maxScore-minScore); if (mr.score <= 0.0) { if (warnOption || warnVerboseOption) { warnCount++; if (warnVerboseOption) verbose(1, "Score too small (raw %.1f scaled %.1f #species %d)," " line %d of %s\n", maf->score, mr.score, slCount(maf->components), mf->lf->lineIx, fileName); } mr.score = 0.001; } if (mr.score > 1.0) mr.score = 1.0; mafCount++; fprintf(f, "%u\t", hFindBin(mr.chromStart, mr.chromEnd)); scoredRefTabOut(&mr, f); mafAliFree(&maf); } mafFileFree(&mf); } errCatchEnd(errCatch); if (errCatch->gotError) { errMsg = cloneString(errCatch->message->string); } errCatchFree(&errCatch); if (errMsg) { if (!isCustom) hgPurgeExtFile(extId, conn); errAbort("%s", errMsg); } if (warnCount) verbose(1, "%d warnings\n", warnCount); } if (testFile != NULL) return; verbose(1, "Loading %s into database\n", table); if (tmpDir == NULL) hgLoadTabFile(conn, ".", table, &f); else hgLoadTabFile(conn, tmpDir, table, &f); verbose(1, "Loaded %ld mafs in %d files from %s\n", mafCount, slCount(fileList), pathPrefix); if (isCustom) sqlDisconnect(&conn); else hgEndUpdate(&conn, 0, 0, "Add %ld mafs in %d files from %s\n", mafCount, slCount(fileList), pathPrefix); /* if temp dir specified, unlink file to make it disappear */ if ((char *)NULL != tmpDir) hgUnlinkTabFile(tmpDir, table); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); warnOption = optionExists("warn"); isCustom = optionExists("custom"); warnVerboseOption = optionExists("WARN"); testFile = optionVal("test", NULL); pathPrefix = optionVal("pathPrefix", NULL); tmpDir = optionVal("tmpDir", NULL); loadFile = optionVal("loadFile", loadFile); refDb = optionVal("refDb", refDb); maxNameLen = optionInt("maxNameLen", maxNameLen); defPosFile = optionVal("defPos", defPosFile); if (argc != 3) usage(); hgLoadMaf(argv[1], argv[2]); return 0; }