src/hg/hgc/bamClick.c 1.7
1.7 2009/08/24 23:47:56 angie
Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
Index: src/hg/hgc/bamClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/bamClick.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/hgc/bamClick.c 22 Aug 2009 02:18:35 -0000 1.6
+++ src/hg/hgc/bamClick.c 24 Aug 2009 23:47:56 -0000 1.7
@@ -1,161 +1,169 @@
/* bamClick - handler for alignments in BAM format (produced by MAQ,
* BWA and some other short-read alignment tools). */
#ifdef USE_BAM
#include "common.h"
#include "hash.h"
#include "hdb.h"
#include "bamFile.h"
#include "hgc.h"
static char const rcsid[] = "$Id$";
#include "bamFile.h"
struct bamTrackData
{
int itemStart;
char *itemName;
struct hash *pairHash;
};
static void singleBamDetails(const bam1_t *bam)
/* Print out the properties of this alignment. */
{
const bam1_core_t *core = &bam->core;
char *itemName = bam1_qname(bam);
int tLength = bamGetTargetLength(bam);
int tStart = core->pos, tEnd = tStart+tLength;
-boolean isRc = ((core->flag & BAM_FREVERSE) != 0);
-printPosOnChrom(seqName, tStart, tEnd, (isRc ? "-" : "+"), FALSE, itemName);
+boolean isRc = bamIsRc(bam);
+printPosOnChrom(seqName, tStart, tEnd, NULL, FALSE, itemName);
printf("<B>Flags: </B><tt>0x%02x</tt><BR>\n", core->flag);
printf("<B>Alignment Quality: </B>%d<BR>\n", core->qual);
-printf("<B>CIGAR string: </B><tt>%s</tt><BR>\n", bamGetCigar(bam));
+printf("<B>CIGAR string: </B><tt>%s</tt> (", bamGetCigar(bam));
+bamShowCigarEnglish(bam);
+printf(")<BR>\n");
+printf("<B>Tags:</B>");
+bamShowTags(bam);
+puts("<BR><BR>");
char nibName[HDB_MAX_PATH_STRING];
hNibForChrom(database, seqName, nibName);
struct dnaSeq *genoSeq = hFetchSeq(nibName, seqName, tStart, tEnd);
struct ffAli *ffa = bamToFfAli(bam, genoSeq, tStart);
char *qSeq = ffa->nStart;
-printf("<BR><B>Alignment of %s to %s:%d-%d%s:</B><BR>\n", itemName,
+printf("<B>Alignment of %s to %s:%d-%d%s:</B><BR>\n", itemName,
seqName, tStart+1, tEnd, (isRc ? " (reverse complemented)" : ""));
ffShowSideBySide(stdout, ffa, qSeq, 0, genoSeq->dna, tStart, tLength, 0, tLength, 8, isRc,
FALSE);
-printf("<B>Tags:</B><BR>\n");
+//TODO: show flags properly, maybe display sequence quality scores
+}
-// ugly: lifted from 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("\t%c%c:", key[0], key[1]);
- if (type == 'A') { printf("A:%c", *s); ++s; }
- else if (type == 'C') { printf("i:%u", *s); ++s; }
- else if (type == 'c') { printf("i:%d", *s); ++s; }
- else if (type == 'S') { printf("i:%u", *(uint16_t*)s); s += 2; }
- else if (type == 's') { printf("i:%d", *(int16_t*)s); s += 2; }
- else if (type == 'I') { printf("i:%u", *(uint32_t*)s); s += 4; }
- else if (type == 'i') { printf("i:%d", *(int32_t*)s); s += 4; }
- else if (type == 'f') { printf("f:%g", *(float*)s); s += 4; }
- else if (type == 'd') { printf("d:%lg", *(double*)s); s += 8; }
- else if (type == 'Z' || type == 'H')
- {
- printf("%c:", (char)type);
- while (*s) putc(*s++, stdout);
- ++s;
- }
+static void showOverlap(const bam1_t *leftBam, const bam1_t *rightBam)
+/* If the two reads overlap, show how. */
+{
+const bam1_core_t *leftCore = &(leftBam->core), *rightCore = &(rightBam->core);
+int leftStart = leftCore->pos, rightStart = rightCore->pos;
+int leftLen = bamGetTargetLength(leftBam), rightLen = bamGetTargetLength(rightBam);
+char *leftSeq = bamGetQuerySequence(leftBam), *rightSeq = bamGetQuerySequence(rightBam);
+if (bamIsRc(leftBam))
+ reverseComplement(leftSeq, strlen(leftSeq));
+if (bamIsRc(rightBam))
+ reverseComplement(rightSeq, strlen(rightSeq));
+if ((rightStart > leftStart && leftStart + leftLen > rightStart) ||
+ (leftStart > rightStart && rightStart+rightLen > leftStart))
+ {
+ printf("<B>Note: End read alignments overlap:</B><BR>\n<PRE><TT>");
+ int i = leftStart - rightStart;
+ while (i-- > 0)
+ putc(' ', stdout);
+ puts(leftSeq);
+ i = rightStart - leftStart;
+ while (i-- > 0)
+ putc(' ', stdout);
+ puts(rightSeq);
+ puts("</TT></PRE>");
}
-//TODO: show flags properly, maybe display sequence quality scores
}
static void bamPairDetails(const bam1_t *leftBam, const bam1_t *rightBam)
/* Print out details for paired-end reads. */
{
//TODO: tell them which one they clicked (match itemStart w/core->pos)
+showOverlap(leftBam, rightBam);
printf("<TABLE><TR><TD><H4>Left end read</H4>\n");
singleBamDetails(leftBam);
printf("</TD><TD><H4>Right end read</H4>\n");
singleBamDetails(rightBam);
printf("</TD></TR></TABLE>\n");
}
static int oneBam(const bam1_t *bam, void *data)
/* This is called on each record retrieved from a .bam file. */
{
const bam1_core_t *core = &bam->core;
if (core->flag & BAM_FUNMAP)
return 0;
struct bamTrackData *btd = (struct bamTrackData *)data;
if (sameString(bam1_qname(bam), btd->itemName))
{
if (btd->pairHash == NULL || (core->flag & BAM_FPAIRED) == 0)
{
if (core->pos == btd->itemStart)
singleBamDetails(bam);
}
else
{
bam1_t *firstBam = (bam1_t *)hashFindVal(btd->pairHash, btd->itemName);
if (firstBam == NULL)
hashAdd(btd->pairHash, btd->itemName, bamClone(bam));
else
{
bamPairDetails(firstBam, bam);
hashRemove(btd->pairHash, btd->itemName);
}
}
}
return 0;
}
void doBamDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a BAM file. */
{
int start = cartInt(cart, "o");
// TODO: libify tdb settings table_pairEndsByName, stripPrefix and pairSearchRange
char varName[1024];
safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->tableName);
boolean isPaired = cartUsualBoolean(cart, varName,
(trackDbSetting(tdb, "pairEndsByName") != NULL));
char *seqNameForBam = seqName;
char *stripPrefix = trackDbSetting(tdb, "stripPrefix");
if (stripPrefix && startsWith(stripPrefix, seqName))
seqNameForBam = seqName + strlen(stripPrefix);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", seqNameForBam, winStart, winEnd);
+bamIgnoreStrand();
struct hash *pairHash = isPaired ? hashNew(0) : NULL;
struct bamTrackData btd = {start, item, pairHash};
bamFetch(database, tdb->tableName, posForBam, oneBam, &btd);
if (isPaired && hashNumEntries(pairHash) > 0)
{
char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "1000");
int pairSearchRange = atoi(setting);
struct hashEl *hel;
struct hashCookie cookie = hashFirst(pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct hash *newPairHash = hashNew(0);
btd.itemName = hel->name;
btd.pairHash = newPairHash;
safef(posForBam, sizeof(posForBam), "%s:%d-%d", seqNameForBam,
winStart-pairSearchRange, winEnd+pairSearchRange);
bamFetch(database, tdb->tableName, posForBam, oneBam, &btd);
if (hashNumEntries(newPairHash) > 0)
{
struct hashCookie cookie2 = hashFirst(pairHash);
while ((hel = hashNext(&cookie2)) != NULL)
{
printf("<B>Note: </B>unable to find paired end "
"for this %s within +-%d of viewing window<BR>\n",
hel->name, pairSearchRange);
singleBamDetails((bam1_t *)hel->val);
}
}
}
}
}
#endif//def USE_BAM