18d303bb4f14e1edff401c8a85276ff1344f0f37
angie
Tue Apr 3 10:18:14 2012 -0700
Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row
declaring its type and annoRow{Free,Clone} taking a numCols argument
that is meaningless for wig, now annoRow{Free,Clone} take the row's
source annoStreamer as an argument. The annoStreamer now has public
members (rowType and numCols) that provide all information needed about
the row. annoStreamer constructors need to set rowType.
diff --git src/lib/vcf.c src/lib/vcf.c
index bece59d..8c8bcac 100644
--- src/lib/vcf.c
+++ src/lib/vcf.c
@@ -615,98 +615,118 @@
}
}
continue;
}
*eq = '\0';
el->key = vcfFilePooledStr(vcff, elStr);
enum vcfInfoType type = typeForInfoKey(vcff, el->key);
char *valStr = eq+1;
el->count = parseInfoValue(record, el->key, type, valStr, &(el->values), &(el->missingData));
if (el->count >= VCF_MAX_INFO)
vcfFileErr(vcff, "A single element of the INFO column has at least %d values; "
"VCF_MAX_INFO may need to be increased in vcf.c!", VCF_MAX_INFO);
}
}
-static void vcfParseData(struct vcfFile *vcff, int maxRecords)
-/* Given a vcfFile into which the header has been parsed, and whose lineFile is positioned
- * at the beginning of a data row, parse and store all data rows from lineFile. */
-{
-if (vcff == NULL)
- return;
-int recCount = 0, expected = 8;
-if (vcff->genotypeCount > 0)
- expected = 9 + vcff->genotypeCount;
-char *words[VCF_MAX_COLUMNS];
-int wordCount;
-while ((wordCount = lineFileChop(vcff->lf, words)) > 0)
+struct vcfRecord *vcfRecordFromRow(struct vcfFile *vcff, char **words)
+/* Parse words from a VCF data line into a VCF record structure. */
{
- if (maxRecords >= 0 && recCount >= maxRecords)
- break;
- lineFileExpectWords(vcff->lf, expected, wordCount);
- struct vcfRecord *record;
- AllocVar(record);
+struct vcfRecord *record = vcfFileAlloc(vcff, sizeof(struct vcfRecord));
record->file = vcff;
record->chrom = vcfFilePooledStr(vcff, words[0]);
record->chromStart = lineFileNeedNum(vcff->lf, words, 1) - 1;
// chromEnd may be overwritten by parseRefAndAlt and parseInfoColumn.
record->chromEnd = record->chromStart+1;
record->name = vcfFilePooledStr(vcff, words[2]);
parseRefAndAlt(vcff, record, words[3], words[4]);
record->qual = vcfFilePooledStr(vcff, words[5]);
parseFilterColumn(vcff, record, words[6]);
parseInfoColumn(vcff, record, words[7]);
if (vcff->genotypeCount > 0)
{
record->format = vcfFilePooledStr(vcff, words[8]);
record->genotypeUnparsedStrings = vcfFileAlloc(vcff,
vcff->genotypeCount * sizeof(char *));
int i;
// Don't bother actually parsing all these until & unless we need the info:
for (i = 0; i < vcff->genotypeCount; i++)
record->genotypeUnparsedStrings[i] = vcfFileCloneStr(vcff, words[9+i]);
}
+return record;
+}
+
+struct vcfRecord *vcfNextRecord(struct vcfFile *vcff)
+/* Parse the words in the next line from vcff into a vcfRecord. Return NULL at end of file.
+ * Note: this does not store record in vcff->records! */
+{
+char *words[VCF_MAX_COLUMNS];
+int wordCount;
+if ((wordCount = lineFileChop(vcff->lf, words)) <= 0)
+ return NULL;
+int expected = 8;
+if (vcff->genotypeCount > 0)
+ expected = 9 + vcff->genotypeCount;
+lineFileExpectWords(vcff->lf, expected, wordCount);
+return vcfRecordFromRow(vcff, words);
+}
+
+static void vcfParseData(struct vcfFile *vcff, int maxRecords)
+/* Given a vcfFile into which the header has been parsed, and whose lineFile is positioned
+ * at the beginning of a data row, parse and store all data rows from lineFile. */
+{
+if (vcff == NULL)
+ return;
+int recCount = 0;
+struct vcfRecord *record;
+while ((record = vcfNextRecord(vcff)) != NULL)
+ {
+ if (maxRecords >= 0 && recCount >= maxRecords)
+ break;
slAddHead(&(vcff->records), record);
recCount++;
}
slReverse(&(vcff->records));
lineFileClose(&(vcff->lf));
}
-struct vcfFile *vcfFileMayOpen(char *fileOrUrl, int maxErr, int maxRecords)
-/* Parse a VCF file into a vcfFile object. If maxErr not zero, then
- * continue to parse until this number of error have been reached. A maxErr
- * less than zero does not stop and reports all errors. */
+struct vcfFile *vcfFileMayOpen(char *fileOrUrl, int maxErr, int maxRecords, boolean parseAll)
+/* Open fileOrUrl and parse VCF header; return NULL if unable.
+ * If parseAll, then read in all lines, parse and store in
+ * vcff->records; if maxErr >= zero, then continue to parse until
+ * there are maxErr+1 errors. A maxErr less than zero does not stop
+ * and reports all errors. */
{
struct lineFile *lf = NULL;
if (startsWith("http://", fileOrUrl) || startsWith("ftp://", fileOrUrl) ||
startsWith("https://", fileOrUrl))
lf = netLineFileOpen(fileOrUrl);
else
lf = lineFileMayOpen(fileOrUrl, TRUE);
struct vcfFile *vcff = vcfFileHeaderFromLineFile(lf, maxErr);
+if (parseAll)
vcfParseData(vcff, maxRecords);
return vcff;
}
struct vcfFile *vcfTabixFileMayOpen(char *fileOrUrl, char *chrom, int start, int end,
int maxErr, int maxRecords)
-/* Parse header and rows within the given position range from a VCF file that has been
- * compressed and indexed by tabix into a vcfFile object; return NULL if or if file has
- * no items in range.
- * If maxErr not zero, then continue to parse until this number of error have been reached.
- * A maxErr less than zero does not stop and reports all errors. */
+/* Open a VCF file that has been compressed and indexed by tabix and
+ * parse VCF header, or return NULL if unable. If chrom is non-NULL,
+ * seek to the position range and parse all lines in range into
+ * vcff->records. If maxErr >= zero, then continue to parse until
+ * there are maxErr+1 errors. A maxErr less than zero does not stop
+ * and reports all errors. */
{
struct lineFile *lf = lineFileTabixMayOpen(fileOrUrl, TRUE);
struct vcfFile *vcff = vcfFileHeaderFromLineFile(lf, maxErr);
if (vcff == NULL)
return NULL;
if (isNotEmpty(chrom) && start != end)
{
if (lineFileSetTabixRegion(lf, chrom, start, end))
vcfParseData(vcff, maxRecords);
}
return vcff;
}
void vcfFileFree(struct vcfFile **pVcff)
/* Free a vcfFile object. */