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/snp/snpLoad/snpCheckClassAndObserved.c src/hg/snp/snpLoad/snpCheckClassAndObserved.c index 805eaf5..086a71c 100644 --- src/hg/snp/snpLoad/snpCheckClassAndObserved.c +++ src/hg/snp/snpLoad/snpCheckClassAndObserved.c @@ -1,329 +1,329 @@ /* 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. */ /* snpCheckClassAndObserved * Use UCSC chromInfo. * * Check class for annotations: * SingleClassBetweenLocType * SingleClassRangeLocType * NamedClassWrongLocType * * Check observed for annotations: * ObservedNotAvailable (obsolete) * ObservedWrongFormat * ObservedWrongSize * ObservedMismatch * * Also note RangeSubstitutionLocTypeExactMatch * * Also note SingleClassTriAllelic and SingleClassQuadAllelic */ #include "common.h" #include "hdb.h" static char *snpDb = NULL; FILE *exceptionFileHandle = NULL; void usage() /* Explain usage and exit. */ { errAbort( "snpCheckClassAndObserved - log exceptions with class and observed\n" "usage:\n" " snpCheckClassAndObserved snpDb \n"); } void writeToExceptionFile(char *chrom, int start, int end, int name, char *exception) { fprintf(exceptionFileHandle, "%s\t%d\t%d\trs%d\t%s\n", chrom, start, end, name, exception); } void checkClass(char *chromName, int start, int end, int snp_id, int loc_type, char *class, char *observed) { char *subString = NULL; /* SingleClass should be loc_type 2 */ if (sameString(class, "single")) { if (loc_type == 1 || loc_type == 4 || loc_type == 5 || loc_type == 6) writeToExceptionFile(chromName, start, end, snp_id, "SingleClassRangeLocType"); if (loc_type == 3) writeToExceptionFile(chromName, start, end, snp_id, "SingleClassBetweenLocType"); } if (sameString(class, "named")) { subString = strstr(observed, "LARGEINSERTION"); if (subString != NULL && loc_type != 3) writeToExceptionFile(chromName, start, end, snp_id, "NamedClassWrongLocType"); subString = strstr(observed, "LARGEDELETION"); if (subString != NULL && loc_type != 1) writeToExceptionFile(chromName, start, end, snp_id, "NamedClassWrongLocType"); } } boolean triAllelic(char *observed) { if (sameString(observed, "A/C/G")) return TRUE; if (sameString(observed, "A/C/T")) return TRUE; if (sameString(observed, "A/G/T")) return TRUE; if (sameString(observed, "C/G/T")) return TRUE; return FALSE; } boolean quadAllelic(char *observed) { if (sameString(observed, "A/C/G/T")) return TRUE; return FALSE; } boolean validSingleObserved(char *observed) { if (sameString(observed, "A/C")) return TRUE; if (sameString(observed, "A/G")) return TRUE; if (sameString(observed, "A/T")) return TRUE; if (sameString(observed, "C/G")) return TRUE; if (sameString(observed, "C/T")) return TRUE; if (sameString(observed, "G/T")) return TRUE; return FALSE; } boolean iupac(char *observed) { int pos = strspn(observed, "ACGT-/"); if (pos != strlen(observed)) { verbose(1, "IUPAC detected in %s\n", observed); return TRUE; } return FALSE; } boolean checkObservedFormat(char *chromName, int start, int end, int snp_id, int loc_type, char *class, char *observed) /* return TRUE if format is valid so downstream checks can continue */ { /* Single class */ if (sameString(class, "single")) { if (quadAllelic(observed)) { writeToExceptionFile(chromName, start, end, snp_id, "SingleClassQuadAllelic"); return TRUE; } if (triAllelic(observed)) { writeToExceptionFile(chromName, start, end, snp_id, "SingleClassTriAllelic"); return TRUE; } if (validSingleObserved(observed)) return TRUE; writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongFormat"); return FALSE; } /* In-dels */ /* First char should be dash, second char should be forward slash. */ /* Only one forward slash. */ /* No IUPAC. */ if (sameString(class, "deletion") || sameString(class, "insertion") || sameString(class, "in-del")) { int slashCount = chopString(observed, "/", NULL, 0); if (strlen(observed) < 2 || slashCount > 2 || observed[0] != '-' || observed[1] != '/' || iupac(observed)) { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongFormat"); return FALSE; } return TRUE; } /* Named. */ if (sameString(class, "named")) { if (observed[0] != '(') { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongFormat"); return FALSE; } return TRUE; } /* Mixed. */ if (sameString(class, "mixed")) { int slashCount = chopString(observed, "/", NULL, 0); if (strlen(observed) < 2 || slashCount < 3 || observed[0] != '-' || observed[1] != '/' || iupac(observed)) { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongFormat"); return FALSE; } return TRUE; } /* Microsat. */ return TRUE; } boolean checkObservedSize(char *chromName, int start, int end, int snp_id, int loc_type, char *class, char *observed) /* This only applies to loc_type range. */ { int observedLen = strlen(observed) - 2; int span = end - start; if (loc_type == 3) return TRUE; /* start with simple deletions */ /* deletions can be range (loc_type 1) or exact (loc_type 2) */ if (sameString(class, "deletion") && (loc_type == 1 || loc_type == 2)) { if (observedLen != span) { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongSize"); return FALSE; } return TRUE; } /* loc_type 4,5,6 */ /* only check for class = 'in-del' */ if (!sameString(class, "in-del")) return TRUE; if (loc_type == 4 && observedLen >= span) { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongSize"); return FALSE; } if (loc_type == 5 && observedLen != span) { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongSize"); return FALSE; } if (loc_type == 6 && observedLen <= span) { writeToExceptionFile(chromName, start, end, snp_id, "ObservedWrongSize"); return FALSE; } return TRUE; } void checkObservedAgainstReference(char *chromName, int start, int end, int snp_id, int loc_type, char *class, char *observed, char *refUCSC, char *refUCSCReverseComp, int orientation) { char *refAllele = NULL; char *subString = NULL; if (orientation == 0) refAllele = cloneString(refUCSC); else refAllele = cloneString(refUCSCReverseComp); if (sameString(class, "single") && loc_type == 2 && strlen(refUCSC) == 1) { subString = strstr(observed, refAllele); if (subString == NULL) writeToExceptionFile(chromName, start, end, snp_id, "ObservedMismatch"); return; } if (sameString(class, "deletion")) { subString = cloneString(observed); subString = subString + 2; if (!sameString(subString, refAllele)) writeToExceptionFile(chromName, start, end, snp_id, "ObservedMismatch"); return; } if (sameString(class, "in-del") && loc_type == 5) { subString = cloneString(observed); subString = subString + 2; if (sameString(subString, refAllele)) writeToExceptionFile(chromName, start, end, snp_id, "RangeSubstitutionLocTypeExactMatch"); } /* todo here: check rangeInsertion and rangeDeletion for substring matches at start and end of observed */ } void doCheckWithLocType(char *chromName) /* check each row for exceptions */ { char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; char tableName[64]; int snp_id = 0; int chromStart = 0; int chromEnd = 0; int loc_type = 0; char *class = NULL; char *observed = NULL; char *refUCSC = NULL; char *refUCSCReverseComp = NULL; int orientation = 0; safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName); if (!hTableExists(tableName)) return; verbose(1, "chrom = %s\n", chromName); sqlSafef(query, sizeof(query), "select snp_id, chromStart, chromEnd, loc_type, class, observed, refUCSC, refUCSCReverseComp, orientation from %s", tableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { snp_id = sqlUnsigned(row[0]); chromStart = sqlUnsigned(row[1]); chromEnd = sqlUnsigned(row[2]); loc_type = sqlUnsigned(row[3]); class = cloneString(row[4]); observed = cloneString(row[5]); refUCSC = cloneString(row[6]);; refUCSCReverseComp = cloneString(row[7]); orientation = sqlUnsigned(row[8]); checkClass(chromName, chromStart, chromEnd, snp_id, loc_type, class, observed); if (sameString(observed, "unknown") || sameString(observed, "lengthTooLong")) { writeToExceptionFile(chromName, chromStart, chromEnd, snp_id, "ObservedNotAvailable"); continue; } if(!checkObservedFormat(chromName, chromStart, chromEnd, snp_id, loc_type, class, observed)) continue; if(!checkObservedSize(chromName, chromStart, chromEnd, snp_id, loc_type, class, observed)) continue; checkObservedAgainstReference(chromName, chromStart, chromEnd, snp_id, loc_type, class, observed, refUCSC, refUCSCReverseComp, orientation); } sqlFreeResult(&sr); hFreeConn(&conn); } int main(int argc, char *argv[]) /* read chrN_snpTmp, log exceptions */ { struct slName *chromList, *chromPtr; if (argc != 2) usage(); snpDb = argv[1]; hSetDb(snpDb); chromList = hAllChromNamesDb(snpDb); exceptionFileHandle = mustOpen("snpCheckClassAndObserved.exceptions", "w"); verbose(1, "checking class and observed ...\n"); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) doCheckWithLocType(chromPtr->name); carefulClose(&exceptionFileHandle); return 0; }