src/hg/lib/bamFile.c 1.1

Index: src/hg/lib/bamFile.c
===================================================================
RCS file: src/hg/lib/bamFile.c
diff -N src/hg/lib/bamFile.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/bamFile.c	27 Jul 2009 21:52:08 -0000	1.1
@@ -0,0 +1,52 @@
+/* bam -- interface to binary alignment format files using Heng Li's samtools lib. */
+
+#ifdef USE_BAM
+
+#include "common.h"
+#include "hdb.h"
+#include "bamFile.h"
+
+static char const rcsid[] = "$Id$";
+
+static char *bbiNameFromTable(struct sqlConnection *conn, char *table)
+/* Return file name from little table. */
+/* This should be libified somewhere sensible -- copied from hgTracks/bedTrack.c. */
+{
+char query[256];
+safef(query, sizeof(query), "select fileName from %s", table);
+char *fileName = sqlQuickString(conn, query);
+if (fileName == NULL)
+    errAbort("Missing fileName in %s table", table);
+return fileName;
+}
+
+void bamFetch(char *db, char *table, char *position, bam_fetch_f callbackFunc, void *callbackData)
+/* Open the .bam file given in db.table, fetch items in the seq:start-end position range,
+ * and call callbackFunc on each bam item retrieved from the file plus callbackData. 
+ * Note: if sequences in .bam file don't begin with "chr" but cart position does, pass in 
+ * cart position + strlen("chr") to match the .bam file sequence names. */
+{
+// TODO: if bamFile is URL, convert URL to path a la UDC, but under udcFuse mountpoint.
+// new hg.conf setting for udcFuse mountpoint/support.
+struct sqlConnection *conn = hAllocConn(db);
+char *bamFileName = bbiNameFromTable(conn, table);
+hFreeConn(&conn);
+
+samfile_t *fh = samopen(bamFileName, "rb", NULL);
+if (fh == NULL)
+    errAbort("samopen(%s, \"rb\") returned NULL", bamFileName);
+
+int chromId, start, end;
+int ret = bam_parse_region(fh->header, position, &chromId, &start, &end);
+if (ret != 0)
+    errAbort("bam_parse_region(%s) failed (%d)", position, ret);
+//?? Could this happen if there is no data on some _random?  can avoid with tdb chromosomes...
+
+bam_index_t *idx = bam_index_load(bamFileName);
+ret = bam_fetch(fh->x.bam, idx, chromId, start, end, callbackData, callbackFunc);
+if (ret != 0)
+    errAbort("bam_fetch(%s, %s (chromId=%d) failed (%d)", bamFileName, position, chromId, ret);
+samclose(fh);
+}
+
+#endif//def USE_BAM