#include <string.h>
#include <errno.h>
#include <sys/stat.h>
+#include <getopt.h>
#include "sam.h"
#include "faidx.h"
#include "kstring.h"
+#include "sam_header.h"
static inline int printw(int c, FILE *fp)
{
typedef struct {
int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
+ int rflag_require, rflag_filter;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
- char *reg, *pl_list;
+ char *reg, *pl_list, *fai_fname;
faidx_t *fai;
void *bed, *rghash;
} mplp_conf_t;
skip = 1;
continue;
}
+ if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+ if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
if (ma->conf->bed) { // test overlap
skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
if (skip) continue;
}
data[i]->conf = conf;
h_tmp = bam_header_read(data[i]->fp);
+ if ( !h_tmp ) {
+ fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+ exit(1);
+ }
data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
bh->l_smpl = s.l;
bh->sname = malloc(s.l);
memcpy(bh->sname, s.s, s.l);
- bh->txt = malloc(strlen(BAM_VERSION) + 64);
- bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
- free(s.s);
+ s.l = 0;
+ ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
+ if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
+ h->dict = sam_header_parse2(h->text);
+ int nseq;
+ const char *tags[] = {"SN","LN","UR","M5",NULL};
+ char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
+ for (i=0; i<nseq; i++)
+ {
+ ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
+ if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
+ if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
+ if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
+ kputs(">\n", &s);
+ }
+ if (tbl) free(tbl);
+ bh->txt = s.s;
+ bh->l_txt = 1 + s.l;
bcf_hdr_sync(bh);
bcf_hdr_write(bp, bh);
bca = bcf_call_init(-1., conf->min_baseQ);
ref16 = bam_nt16_table[_ref0];
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
- bcf_call_combine(gplp.n, bcr, ref16, &bc);
+ bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0);
bcf_write(bp, bh, b);
bcf_destroy(b);
if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && 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) {
+ if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
b = calloc(1, sizeof(bcf1_t));
bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref);
bcf_write(bp, bh, b);
}
#define MAX_PATH_LEN 1024
-static int read_file_list(const char *file_list,int *n,char **argv[])
+int read_file_list(const char *file_list,int *n,char **argv[])
{
char buf[MAX_PATH_LEN];
int len, nfiles = 0;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV")) >= 0) {
+ static struct option lopts[] =
+ {
+ {"rf",1,0,1}, // require flag
+ {"ff",1,0,2}, // filter flag
+ {0,0,0,0}
+ };
+ while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
switch (c) {
+ case 1 : mplp.rflag_require = strtol(optarg,0,0); break;
+ case 2 : mplp.rflag_filter = strtol(optarg,0,0); break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
+ mplp.fai_fname = optarg;
break;
case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
fprintf(stderr, " -R ignore RG tags\n");
fprintf(stderr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(stderr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+ fprintf(stderr, " --rf INT required flags: skip reads with mask bits unset []\n");
+ fprintf(stderr, " --ff INT filter flags: skip reads with mask bits set []\n");
fprintf(stderr, "\nOutput options:\n\n");
fprintf(stderr, " -D output per-sample DP in BCF (require -g/-u)\n");
fprintf(stderr, " -g generate BCF output (genotype likelihoods)\n");