typedef struct {
int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
typedef struct {
int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
static int mplp_func(void *data, bam1_t *b)
{
extern int bam_realn(bam1_t *b, const char *ref);
static int mplp_func(void *data, bam1_t *b)
{
extern int bam_realn(bam1_t *b, const char *ref);
extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
if (ret < 0) break;
skip = 0;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
if (ret < 0) break;
skip = 0;
if (has_ref && ma->capQ_thres > 10) {
int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
if (q < 0) skip = 1;
if (has_ref && ma->capQ_thres > 10) {
int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
if (q < 0) skip = 1;
bca = bcf_call_init(-1., conf->min_baseQ);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
bca->rghash = rghash;
bca = bcf_call_init(-1., conf->min_baseQ);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
bca->rghash = rghash;
- if (bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
+ if (!(conf->flag&MPLP_NO_INDEL) && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
case 'R': mplp.flag |= MPLP_REALN; break;
case 'D': mplp.flag |= MPLP_FMT_DP; break;
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'R': mplp.flag |= MPLP_REALN; break;
case 'D': mplp.flag |= MPLP_FMT_DP; break;
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'Q': mplp.min_baseQ = atoi(optarg); break;
case 'b': file_list = optarg; break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'Q': mplp.min_baseQ = atoi(optarg); break;
case 'b': file_list = optarg; break;
fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(stderr, " -d INT max per-sample depth [%d]\n", mplp.max_depth);
fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(stderr, " -d INT max per-sample depth [%d]\n", mplp.max_depth);
fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
+ fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+ fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
+ fprintf(stderr, " -h INT coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");
fprintf(stderr, " -D output per-sample DP\n");
fprintf(stderr, " -S output per-sample SP (strand bias P-value, slow)\n");
fprintf(stderr, " -g generate BCF output\n");
fprintf(stderr, " -u do not compress BCF output\n");
fprintf(stderr, " -B disable BAQ computation\n");
fprintf(stderr, " -D output per-sample DP\n");
fprintf(stderr, " -S output per-sample SP (strand bias P-value, slow)\n");