void edwBamToWig(char *input, char *output)
/* edwBamToWig - Convert a bam file to a wig file by measuring depth of coverage, optionally adjusting hit size to average for library.. */
{
FILE *f = mustOpen(output, "w");
/* Open file and get header for it. */
samfile_t *sf = samopen(input, "rb", NULL);
if (sf == NULL)
errnoAbort("Couldn't open %s.\n", input);
bam_header_t *head = sf->header;
if (head == NULL)
errAbort("Aborting ... Bad BAM header in file: %s", input);
/* Scan through input populating genome range trees */
struct genomeRangeTree *grt = genomeRangeTreeNew();
bam1_t one = {};
for (;;)
{
/* Read next record. */
if (bam_read1(sf->x.bam, &one) < 0)
break;
if (one.core.tid >= 0 && one.core.n_cigar > 0)
{
char *chrom = head->target_name[one.core.tid];
int start = one.core.pos;
int end = start + one.core.l_qseq;
if (one.core.flag & BAM_FREVERSE)
{
start -= clPad;
}
else
{
end += clPad;
}
struct rbTree *rt = genomeRangeTreeFindOrAddRangeTree(grt,chrom);
rangeTreeAddToCoverageDepth(rt, start, end);
}
}
/* Convert genome range tree into output wig */
/* Get list of chromosomes. */
struct hashEl *hel, *helList = hashElListHash(grt->hash);
for (hel = helList; hel != NULL; hel = hel->next)
{
char *chrom = hel->name;
struct rbTree *rt = hel->val;
struct range *range, *rangeList = rangeTreeList(rt);
for (range = rangeList; range != NULL; range = range->next)
{
fprintf(f, "%s\t%d\t%d\t%d\n", chrom, range->start, range->end, ptToInt(range->val));
}
}
carefulClose(&f);
}
struct genomeRangeTree *edwGrtFromBigBed(char *fileName)
/* Return genome range tree for simple (unblocked) bed */
{
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
struct genomeRangeTree *grt = genomeRangeTreeNew();
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
struct rbTree *tree = genomeRangeTreeFindOrAddRangeTree(grt, chrom->name);
struct lm *lm = lmInit(0);
struct bigBedInterval *iv, *ivList = NULL;
ivList = bigBedIntervalQuery(bbi, chrom->name, 0, chrom->size, 0, lm);
for (iv = ivList; iv != NULL; iv = iv->next)
rangeTreeAdd(tree, iv->start, iv->end);
lmCleanup(&lm);
}
bigBedFileClose(&bbi);
bbiChromInfoFreeList(&chromList);
return grt;
}
struct range *genomeRangeTreeAdd(struct genomeRangeTree *tree, char *chrom, int start, int end)
/* Add range to tree, merging with existing ranges if need be.
* Adds new rangeTree if chrom not found. */
{
return rangeTreeAdd(genomeRangeTreeFindOrAddRangeTree(tree,chrom), start, end);
}
