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)
case '=': // match
case 'X': // mismatch
tLength += n;
break;
case 'I': // inserted in query
break;
case 'D': // deleted from query
case 'N': // long deletion from query (intron as opposed to small del)
tLength += n;
break;
case 'S': // skipped query bases at beginning or end ("soft clipping")
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,
boolean useStrand, char **retQSeq)
/* Convert from bam to ffAli format. If retQSeq is non-null, set it to the
* query sequence into which ffAli needle pointers point. (Adapted from psl.c's pslToFfAli.) */
{
struct ffAli *ffList = NULL, *ff;
const bam1_core_t *core = &bam->core;
boolean isRc = useStrand && bamIsRc(bam);
DNA *needle = (DNA *)bamGetQuerySequence(bam, useStrand);
if (retQSeq)
*retQSeq = needle;
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)
case '=': // match
case 'X': // mismatch
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;
}
void bamGetSoftClipping(const bam1_t *bam, int *retLow, int *retHigh, int *retClippedQLen)
/* If retLow is non-NULL, set it to the number of "soft-clipped" (skipped) bases at
* the beginning of the query sequence and quality; likewise for retHigh at end.
* For convenience, retClippedQLen is the original query length minus soft clipping
* (and the length of the query sequence that will be returned). */
{
unsigned int *cigarPacked = bam1_cigar(bam);
const bam1_core_t *core = &bam->core;
char op;
int n = bamUnpackCigarElement(cigarPacked[0], &op);
int low = (op == 'S') ? n : 0;
n = bamUnpackCigarElement(cigarPacked[core->n_cigar-1], &op);
int high = (op == 'S') ? n : 0;
if (retLow != NULL)
*retLow = low;
if (retHigh != NULL)
*retHigh = high;
if (retClippedQLen != NULL)
*retClippedQLen = (core->l_qseq - low - high);
}
void bamUnpackCigar(const bam1_t *bam, struct dyString *dyCigar)
/* Unpack CIGAR string into dynamic string */
{
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);
dyStringPrintf(dyCigar, "%d", n);
dyStringAppendC(dyCigar, op);
}
}
static int countBam(const bam1_t *bam, void *data)
/* bam_fetch() calls this on each bam alignment retrieved. */
{
struct bamWigTrackData *btd = (struct bamWigTrackData *)data;
const bam1_core_t *core = &bam->core;
int tLength=0, tPos = core->pos, qPos = 0;
unsigned int *cigar = bam1_cigar(bam);
int i;
double scale = btd->scale;
for (i = 0; i < core->n_cigar; i++)
{
char op;
int n = bamUnpackCigarElement(cigar[i], &op);
switch (op)
{
case 'X': // mismatch (gapless aligned block)
case '=': // match (gapless aligned block)
case 'M': // match or mismatch (gapless aligned block)
{
int start = (int)(scale * (tPos - winStart));
int end = (int)(scale * ((tPos + n) - winStart));
for(i=start; i < end; i++)
btd->preDraw[i + btd->preDrawZero].count++;
tPos = tPos + n;
qPos = qPos + n;
tLength += n;
break;
}
case 'I': // inserted in query
qPos += n;
break;
case 'D': // deleted from query
case 'N': // long deletion from query (intron as opposed to small del)
tPos += n;
tLength += n;
break;
case 'S': // skipped query bases at beginning or end ("soft clipping")
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("countBam: unrecognized CIGAR op %c -- update me", op);
}
}
return 0;
}
struct simpleFeature *sfFromNumericCigar(const bam1_t *bam, int *retLength)
/* Translate BAM's numeric CIGAR encoding into a list of simpleFeatures,
* and tally up length on reference sequence while we're at it. */
{
const bam1_core_t *core = &bam->core;
struct simpleFeature *sf, *sfList = NULL;
int tLength=0, tPos = core->pos, qPos = 0;
unsigned int *cigar = bam1_cigar(bam);
int i;
for (i = 0; i < core->n_cigar; i++)
{
char op;
int n = bamUnpackCigarElement(cigar[i], &op);
switch (op)
{
case 'X': // mismatch (gapless aligned block)
case '=': // match (gapless aligned block)
case 'M': // match or mismatch (gapless aligned block)
AllocVar(sf);
sf->start = tPos;
sf->qStart = qPos;
tPos = sf->end = tPos + n;
qPos = sf->qEnd = qPos + n;
slAddHead(&sfList, sf);
tLength += n;
break;
case 'I': // inserted in query
qPos += n;
break;
case 'D': // deleted from query
case 'N': // long deletion from query (intron as opposed to small del)
tPos += n;
tLength += n;
break;
case 'S': // skipped query bases at beginning or end ("soft clipping")
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("sfFromNumericCigar: unrecognized CIGAR op %c -- update me", op);
}
}
if (retLength != NULL)
*retLength = tLength;
slReverse(&sfList);
return sfList;
}
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 '=': // match
printf("%d Match", n);
break;
case 'X': // mismatch
printf("%d Mismatch", 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);
}
}
}
static struct psl *pslFromBam(const bam1_t *bam)
/* Translate BAM's numeric CIGAR encoding into PSL sufficient for cds.c (just coords,
* no scoring info) */
{
const bam1_core_t *core = &bam->core;
struct psl *psl;
AllocVar(psl);
boolean isRc = (core->flag & BAM_FREVERSE);
psl->strand[0] = isRc ? '-' : '+';
psl->qName = cloneString(bam1_qname(bam));
psl->tName = cloneString(chromName);
unsigned blockCount = 0;
unsigned *blockSizes, *qStarts, *tStarts;
AllocArray(blockSizes, core->n_cigar);
AllocArray(qStarts, core->n_cigar);
AllocArray(tStarts, core->n_cigar);
int tPos = core->pos, qPos = 0, qLength = 0;
unsigned int *cigar = bam1_cigar(bam);
int i;
for (i = 0; i < core->n_cigar; i++)
{
char op;
int n = bamUnpackCigarElement(cigar[i], &op);
switch (op)
{
case 'X': // mismatch (gapless aligned block)
case '=': // match (gapless aligned block)
case 'M': // match or mismatch (gapless aligned block)
blockSizes[blockCount] = n;
qStarts[blockCount] = qPos;
tStarts[blockCount] = tPos;
blockCount++;
tPos += n;
qPos += n;
qLength += n;
break;
case 'I': // inserted in query
qPos += n;
qLength += n;
break;
case 'D': // deleted from query
case 'N': // long deletion from query (intron as opposed to small del)
tPos += n;
break;
case 'S': // skipped query bases at beginning or end ("soft clipping")
qPos += n;
qLength += 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("pslFromBam: unrecognized CIGAR op %c -- update me", op);
}
}
if (blockCount == 0)
{
// sometimes BAM's have alignments with no alignment
return NULL; // leaks allocated PSL.
}
psl->tSize = hChromSize(database, chromName);
psl->tStart = tStarts[0];
psl->tEnd = tStarts[blockCount-1] + blockSizes[blockCount-1];
psl->qSize = qLength;
psl->qStart = qStarts[0];
psl->qEnd = qStarts[blockCount-1] + blockSizes[blockCount-1];
if (isRc)
reverseIntRange(&psl->qStart, &psl->qEnd, psl->qSize);
psl->blockCount = blockCount;
psl->blockSizes = blockSizes;
psl->qStarts = qStarts;
psl->tStarts = tStarts;
return psl;
}
