void filterReads(char * inBamFile,
char * outBamFile,
int minMapQual,
int minLen,
int maxMisMatches,
float minPcId,
float minPcAln,
int ignoreSuppAlignments,
int ignoreSecondaryAlignments) {
//
int result = -1;
int outResult = -1;
int supp_check = 0x0;
if (ignoreSuppAlignments) {
supp_check |= BAM_FSUPPLEMENTARY;
}
if (ignoreSecondaryAlignments) {
supp_check |= BAM_FSECONDARY;
}
// helper variables
BGZF* in = 0;
BGZF* out = 0;
bam1_t *b = bam_init1();
bam_hdr_t *h;
// open bam
if ((in = bgzf_open(inBamFile, "r")) == 0) {
fprintf(stderr,
"ERROR: Failed to open \"%s\" for reading.\n",
inBamFile);
}
else if ((h = bam_hdr_read(in)) == 0) { // read header
fprintf(stderr,
"ERROR: Failed to read BAM header of file \"%s\".\n",
inBamFile);
}
else if ((out = bgzf_open(outBamFile, "w")) == 0) {
fprintf(stderr,
"ERROR: Failed to open \"%s\" for writing.\n",
outBamFile);
}
else {
// write and destroy header
bam_hdr_write(out, h);
bam_hdr_destroy(h);
int line = 0;
int matches, mismatches, qLen;
float pcAln, pcId;
int showStats = 0;
// fetch alignments
while ((result = bam_read1(in, b)) >= 0) {
line += 1;
// only primary mappings
if ((b->core.flag & supp_check) != 0) {
if (showStats)
fprintf(stdout, "Rejected %d, non-primary\n", line);
continue;
}
// only high quality
if (b->core.qual < minMapQual) {
if (showStats)
fprintf(stdout, "Rejected %d, quality: %d\n", line, b->core.qual);
continue;
}
// not too many absolute mismatches
mismatches = bam_aux2i(bam_aux_get(b, "NM"));
if (mismatches > maxMisMatches) {
if (showStats)
fprintf(stdout, "Rejected %d, mismatches: %d\n", line, mismatches);
continue;
}
// not too short
qLen = bam_cigar2qlen((&b->core)->n_cigar, bam_get_cigar(b));
if (qLen < minLen) {
if (showStats)
fprintf(stdout, "Rejected %d, length: %d\n", line, qLen);
continue;
}
// only high percent identity
matches = bam_cigar2matches((&b->core)->n_cigar, bam_get_cigar(b));
pcId = (matches - mismatches) / (float)matches; // percentage as float between 0 to 1
if (pcId < minPcId) {
if (showStats)
fprintf(stdout, "Rejected %d, identity pc: %.4f\n", line, pcId);
continue;
}
// only high percent alignment
pcAln = matches / (float)qLen; // percentage as float between 0 to 1
if (pcAln < minPcAln) {
if (showStats)
fprintf(stdout, "Rejected %d, alignment pc: %.4f\n", line, pcAln);
continue;
}
if ((outResult = bam_write1(out, b)) < -1) {
fprintf(stderr,
"ERROR: Attempt to write read no. %d to file \"%s\" failed with code %d.\n",
line, outBamFile, outResult);
}
}
if (result < -1) {
fprintf(stderr,
"ERROR: retrieval of read no. %d from file \"%s\" failed with code %d.\n",
line, inBamFile, result);
}
}
if (in) bgzf_close(in);
if (out) bgzf_close(out);
bam_destroy1(b);
}
void profileReads(char* bamFile,
int ignoreSuppAlignments,
int ignoreSecondaryAlignments) {
//
int result = -1;
int supp_check = 0x0;
if (ignoreSuppAlignments) {
supp_check |= BAM_FSUPPLEMENTARY;
}
if (ignoreSecondaryAlignments) {
supp_check |= BAM_FSECONDARY;
}
// helper variables
BGZF* in = 0 ;
bam1_t *b = bam_init1();
bam_hdr_t *h;
// open bam
if ((in = bgzf_open(bamFile, "r")) == 0) {
fprintf(stderr,
"ERROR: Failed to open \"%s\" for reading.\n",
bamFile);
}
else if ((h = bam_hdr_read(in)) == 0) { // read header
fprintf(stderr,
"ERROR: Failed to read BAM header of file \"%s\".\n",
bamFile);
}
else {
// destroy header
bam_hdr_destroy(h);
int line = 0;
int supplementary, secondary;
int mapQual;
int matches, mismatches, qLen;
float pcAln, pcId;
int showStats = 0;
uint8_t *aux_mismatches;
// print header
printf("line\tsupp\tsecondary\tmapQ\tmismatches\tmatches\tqLen\tpcId\tpcAln\n");
// fetch alignments
while ((result = bam_read1(in, b)) >= 0) {
line += 1;
// only primary mappings
if ((b->core.flag & supp_check) != 0) {
if (showStats)
fprintf(stdout, "Rejected %d, non-primary\n", line);
continue;
}
supplementary = (b->core.flag & (1 | BAM_FSUPPLEMENTARY)) != 0;
secondary = (b->core.flag & (1 | BAM_FSECONDARY)) != 0;
// quality
mapQual = b->core.qual;
// bam_aux_get returns 0 if optional NM tag is missing
if ((aux_mismatches = bam_aux_get(b, "NM")))
mismatches = bam_aux2i(aux_mismatches);
else
mismatches = 0;
// length
qLen = bam_cigar2qlen((&b->core)->n_cigar, bam_get_cigar(b));
// percent identity
matches = bam_cigar2matches((&b->core)->n_cigar, bam_get_cigar(b));
pcId = (matches - mismatches) / (float)matches; // percentage as float between 0 to 1
// percent alignment
pcAln = matches / (float)qLen; // percentage as float between 0 to 1
// print read values
printf("%d\t%d\t%d\t%d\t%d\t%d\t%d\t%.4f\t%.4f\n",
line, supplementary, secondary, mapQual, mismatches, matches,
qLen, pcId, pcAln);
}
if (result < -1) {
fprintf(stderr,
"ERROR: retrieval of read no. %d from file \"%s\" failed with code %d.\n",
line, bamFile, result);
}
}
if (in) bgzf_close(in);
bam_destroy1(b);
}
