struct genomeRangeTree *edwMakeGrtFromBed3List(struct bed3 *bedList)
/* Make up a genomeRangeTree around bed file. */
{
struct genomeRangeTree *grt = genomeRangeTreeNew();
struct bed3 *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
genomeRangeTreeAdd(grt, bed->chrom, bed->chromStart, bed->chromEnd);
return grt;
}
struct genomeRangeTree* getRangeTreeOfRegdoms(struct regdom* regdoms)
{
struct genomeRangeTree *ranges = genomeRangeTreeNew();
struct regdom* currRD;
for (currRD = regdoms; currRD != NULL; currRD = currRD->next) {
genomeRangeTreeAdd(ranges, currRD->chrom, currRD->chromStart, currRD->chromEnd);
}
return ranges;
}
struct genomeRangeTree *grtFromOpenBed(struct lineFile *lf, int size, boolean doPromoter)
/* Read an open bed file into a genomeRangeTree and return it. */
{
struct genomeRangeTree *grt = genomeRangeTreeNew();
char *row[size];
while (lineFileRow(lf, row))
{
struct bed *bed = bedLoadN(row, size);
if (doPromoter)
{
if (bed->strand[0] == '+')
genomeRangeTreeAdd(grt, bed->chrom, bed->chromStart - 500, bed->chromEnd + 500);
else
genomeRangeTreeAdd(grt, bed->chrom, bed->chromEnd - 500, bed->chromEnd + 500);
}
else
genomeRangeTreeAdd(grt, bed->chrom, bed->chromStart, bed->chromEnd);
}
return grt;
}
static void scanSam(char *samIn, FILE *f, struct genomeRangeTree *grt, long long *retHit,
long long *retMiss, long long *retTotalBasesInHits)
/* Scan through sam file doing several things:counting how many reads hit and how many
* miss target during mapping phase, copying those that hit to a little bed file, and
* also defining regions covered in a genomeRangeTree. */
{
samfile_t *sf = samopen(samIn, "r", NULL);
bam_header_t *bamHeader = sf->header;
bam1_t one;
ZeroVar(&one);
int err;
long long hit = 0, miss = 0, totalBasesInHits = 0;
while ((err = samread(sf, &one)) >= 0)
{
int32_t tid = one.core.tid;
if (tid < 0)
{
++miss;
continue;
}
++hit;
char *chrom = bamHeader->target_name[tid];
// Approximate here... can do better if parse cigar.
int start = one.core.pos;
int size = one.core.l_qseq;
int end = start + size;
totalBasesInHits += size;
boolean isRc = (one.core.flag & BAM_FREVERSE);
char strand = '+';
if (isRc)
{
strand = '-';
reverseIntRange(&start, &end, bamHeader->target_len[tid]);
}
if (start < 0) start=0;
if (f != NULL)
fprintf(f, "%s\t%d\t%d\t.\t0\t%c\n", chrom, start, end, strand);
genomeRangeTreeAdd(grt, chrom, start, end);
}
if (err < 0 && err != -1)
errnoAbort("samread err %d", err);
samclose(sf);
*retHit = hit;
*retMiss = miss;
*retTotalBasesInHits = totalBasesInHits;
}
static void subset_with_sections(struct metaBig* mb, struct bed** p_list)
/* mainly for chopgenome */
{
struct genomeRangeTree* grt = genomeRangeTreeNew();
struct bed* sec;
struct bed* list;
struct bed* newlist = NULL;
struct bed* head;
for (sec = mb->sections; sec != NULL; sec = sec->next)
genomeRangeTreeAdd(grt, sec->chrom, sec->chromStart, sec->chromEnd);
list = *p_list;
while ((head = slPopHead(&list)) != NULL) {
if (genomeRangeTreeOverlaps(grt, head->chrom, head->chromStart, head->chromEnd) && genomeRangeTreeFindEnclosing(grt, head->chrom, head->chromStart, head->chromEnd))
slAddHead(&newlist, head);
else
bedFree(&head);
}
slReverse(&newlist);
*p_list = newlist;
}
