src/hg/lib/bamFile.c 1.6
1.6 2009/08/24 23:47:56 angie
Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
Index: src/hg/lib/bamFile.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/bamFile.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/lib/bamFile.c 21 Aug 2009 22:52:35 -0000 1.5
+++ src/hg/lib/bamFile.c 24 Aug 2009 23:47:56 -0000 1.6
@@ -1,180 +1,267 @@
/* 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 boolean ignoreStrand = FALSE;
+
+void bamIgnoreStrand()
+/* Change the behavior of this lib to disregard item strand.
+ * If called, this should be called before any other bam functions. */
+{
+ignoreStrand = TRUE;
+}
+
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);
}
+boolean bamIsRc(const bam1_t *bam)
+/* Return TRUE if alignment is on - strand. If bamIgnoreStrand has been called,
+ * then this always returns FALSE. */
+{
+const bam1_core_t *core = &bam->core;
+return (core->flag & BAM_FREVERSE) && !ignoreStrand;
+}
+
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))
+if (bamIsRc(bam))
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);
}
+void bamShowCigarEnglish(const bam1_t *bam)
+/* Print out cigar in English e.g. "20 (mis)Match, 1 Deletion, 3 (mis)Match" */
+{
+unsigned int *cigarPacked = bam1_cigar(bam);
+const bam1_core_t *core = &bam->core;
+int i;
+for (i = 0; i < core->n_cigar; i++)
+ {
+ char op;
+ int n = bamUnpackCigarElement(cigarPacked[i], &op);
+ if (i > 0)
+ printf(", ");
+ switch (op)
+ {
+ case 'M': // match or mismatch (gapless aligned block)
+ printf("%d (mis)Match", n);
+ break;
+ case 'I': // inserted in query
+ printf("%d Insertion", n);
+ break;
+ case 'S': // skipped query bases at beginning or end ("soft clipping")
+ printf("%d Skipped", n);
+ break;
+ case 'D': // deleted from query
+ printf("%d Deletion", n);
+ break;
+ case 'N': // long deletion from query (intron as opposed to small del)
+ printf("%d deletioN", n);
+ break;
+ case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
+ printf("%d Hard clipped query", n);
+ break;
+ case 'P': // P="silent deletion from padded reference sequence"
+ printf("%d Padded / silent deletion", n);
+ break;
+ default:
+ errAbort("bamShowCigarEnglish: unrecognized CIGAR op %c -- update me", op);
+ }
+ }
+}
+
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);
+boolean isRc = bamIsRc(bam);
DNA *needle = (DNA *)bamGetQuerySequence(bam);
if (isRc)
reverseComplement(target->dna, target->size);
DNA *haystack = target->dna;
unsigned int *cigarPacked = bam1_cigar(bam);
int tStart = targetOffset, qStart = 0, i;
// If isRc, need to go through the CIGAR ops backwards, but sequence offsets still count up.
int iStart = isRc ? (core->n_cigar - 1) : 0;
int iIncr = isRc ? -1 : 1;
for (i = iStart; isRc ? (i >= 0) : (i < core->n_cigar); i += iIncr)
{
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;
}
bam1_t *bamClone(const bam1_t *bam)
/* Return a newly allocated copy of bam. */
{
// Using typecasts to get around compiler complaints about bam being const:
bam1_t *newBam = cloneMem((void *)bam, sizeof(*bam));
newBam->data = cloneMem((void *)bam->data, bam->data_len*sizeof(bam->data[0]));
return newBam;
}
+void bamShowTags(const bam1_t *bam)
+/* Print out tags in HTML: bold key, no type indicator for brevity. */
+{
+// adapted from part of bam.c bam_format1:
+uint8_t *s = bam1_aux(bam);
+while (s < bam->data + bam->data_len)
+ {
+ uint8_t type, key[2];
+ key[0] = s[0]; key[1] = s[1];
+ s += 2; type = *s; ++s;
+ printf(" <B>%c%c</B>:", key[0], key[1]);
+ if (type == 'A') { printf("%c", *s); ++s; }
+ else if (type == 'C') { printf("%u", *s); ++s; }
+ else if (type == 'c') { printf("%d", *s); ++s; }
+ else if (type == 'S') { printf("%u", *(uint16_t*)s); s += 2; }
+ else if (type == 's') { printf("%d", *(int16_t*)s); s += 2; }
+ else if (type == 'I') { printf("%u", *(uint32_t*)s); s += 4; }
+ else if (type == 'i') { printf("%d", *(int32_t*)s); s += 4; }
+ else if (type == 'f') { printf("%g", *(float*)s); s += 4; }
+ else if (type == 'd') { printf("%lg", *(double*)s); s += 8; }
+ else if (type == 'Z' || type == 'H')
+ {
+ while (*s) putc(*s++, stdout);
+ ++s;
+ }
+ }
+putc('\n', stdout);
+}
+
#endif//def USE_BAM