src/hg/lib/bamFile.c 1.4
1.4 2009/08/21 05:22:01 angie
Added bamToFfAli (for using fuzzyShow display).
Index: src/hg/lib/bamFile.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/bamFile.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/lib/bamFile.c 3 Aug 2009 22:14:39 -0000 1.3
+++ src/hg/lib/bamFile.c 21 Aug 2009 05:22:01 -0000 1.4
@@ -1,119 +1,168 @@
/* 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);
}
char *bamGetQuerySequence(const bam1_t *bam)
/* Return the nucleotide sequence encoded in bam. The BAM format
* reverse-complements query sequence when the alignment is on the - strand,
* so here we rev-comp it back to restore the original query sequence. */
{
const bam1_core_t *core = &bam->core;
char *qSeq = needMem(core->l_qseq + 1);
uint8_t *s = bam1_seq(bam);
int i;
for (i = 0; i < core->l_qseq; i++)
qSeq[i] = bam_nt16_rev_table[bam1_seqi(s, i)];
if ((core->flag & BAM_FREVERSE))
reverseComplement(qSeq, core->l_qseq);
return qSeq;
}
char *bamGetCigar(const bam1_t *bam)
/* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */
{
unsigned int *cigarPacked = bam1_cigar(bam);
const bam1_core_t *core = &bam->core;
struct dyString *dyCigar = dyStringNew(min(8, core->n_cigar*4));
int i;
for (i = 0; i < core->n_cigar; i++)
{
char op;
int n = bamUnpackCigarElement(cigarPacked[i], &op);
dyStringPrintf(dyCigar, "%d", n);
dyStringAppendC(dyCigar, op);
}
return dyStringCannibalize(&dyCigar);
}
int bamGetTargetLength(const bam1_t *bam)
/* Tally up the alignment's length on the reference sequence from
* bam's packed-int CIGAR representation. */
{
unsigned int *cigarPacked = bam1_cigar(bam);
const bam1_core_t *core = &bam->core;
int tLength=0;
int i;
for (i = 0; i < core->n_cigar; i++)
{
char op;
int n = bamUnpackCigarElement(cigarPacked[i], &op);
switch (op)
{
case 'M': // match or mismatch (gapless aligned block)
tLength += n;
break;
case 'I': // inserted in query
case 'S': // skipped query bases at beginning or end ("soft clipping")
break;
case 'D': // deleted from query
case 'N': // long deletion from query (intron as opposed to small del)
tLength += n;
break;
case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
case 'P': // P="silent deletion from padded reference sequence" -- ignore these.
break;
default:
errAbort("bamGetTargetLength: unrecognized CIGAR op %c -- update me", op);
}
}
return tLength;
}
+struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset)
+/* Convert from bam to ffAli format. (Adapted from psl.c's pslToFfAli.) */
+{
+struct ffAli *ffList = NULL, *ff;
+const bam1_core_t *core = &bam->core;
+boolean isRc = ((core->flag & BAM_FREVERSE) != 0);
+DNA *needle = (DNA *)bamGetQuerySequence(bam);
+if (isRc)
+ reverseComplement(needle, strlen(needle));
+DNA *haystack = target->dna;
+unsigned int *cigarPacked = bam1_cigar(bam);
+int tStart, qStart, i;
+for (tStart = targetOffset, qStart = 0, i = 0; i < core->n_cigar; i++)
+ {
+ char op;
+ int size = bamUnpackCigarElement(cigarPacked[i], &op);
+ switch (op)
+ {
+ case 'M': // match or mismatch (gapless aligned block)
+ AllocVar(ff);
+ ff->left = ffList;
+ ffList = ff;
+ ff->nStart = needle + qStart;
+ ff->nEnd = ff->nStart + size;
+ ff->hStart = haystack + tStart - targetOffset;
+ ff->hEnd = ff->hStart + size;
+ tStart += size;
+ qStart += size;
+ break;
+ case 'I': // inserted in query
+ case 'S': // skipped query bases at beginning or end ("soft clipping")
+ qStart += size;
+ break;
+ case 'D': // deleted from query
+ case 'N': // long deletion from query (intron as opposed to small del)
+ tStart += size;
+ break;
+ case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
+ case 'P': // P="silent deletion from padded reference sequence" -- ignore these.
+ break;
+ default:
+ errAbort("bamToFfAli: unrecognized CIGAR op %c -- update me", op);
+ }
+ }
+ffList = ffMakeRightLinks(ffList);
+ffCountGoodEnds(ffList);
+return ffList;
+}
+
#endif//def USE_BAM