minor changes. It is BUGGY now!

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 53972de86f62bb717872d1cf6f4b651aac13ba4b..1205e10b845288f25dbd240b3b612ae79d2f8b8a 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -456,6 +456,9 @@ int bam_pileup(int argc, char *argv[])
 
 #define MPLP_GLF   0x10
 #define MPLP_NO_COMP 0x20
+#define MPLP_NO_ORPHAN 0x40
+#define MPLP_REALN   0x80
+#define MPLP_NO_HALFTRIM 0x100
 
 typedef struct {
        int max_mq, min_mq, flag, min_baseQ;
@@ -468,7 +471,8 @@ typedef struct {
 typedef struct {
        bamFile fp;
        bam_iter_t iter;
-       int min_mq;
+       int min_mq, flag;
+       char *ref;
 } mplp_aux_t;
 
 typedef struct {
@@ -479,11 +483,17 @@ typedef struct {
 
 static int mplp_func(void *data, bam1_t *b)
 {
+       extern int bam_realn(bam1_t *b, const char *ref);
        mplp_aux_t *ma = (mplp_aux_t*)data;
-       int ret;
+       int ret, cond = 0;
        do {
+               cond = 0;
                ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
-       } while (b->core.qual < ma->min_mq && ret >= 0);
+               if (ret < 0) break;
+               if (b->core.qual < ma->min_mq) cond = 1; 
+               else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) cond = 1;
+               if (ma->ref && !cond && (ma->flag&MPLP_REALN)) bam_realn(b, ma->ref);
+       } while (cond);
        return ret;
 }
 
@@ -543,6 +553,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                bam_header_t *h_tmp;
                data[i] = calloc(1, sizeof(mplp_aux_t));
                data[i]->min_mq = conf->min_mq;
+               data[i]->flag = conf->flag;
                data[i]->fp = bam_open(fn[i], "r");
                h_tmp = bam_header_read(data[i]->fp);
                bam_smpl_add(sm, fn[i], h_tmp->text);
@@ -614,6 +625,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                if (tid != ref_tid) {
                        free(ref);
                        if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
+                       for (i = 0; i < n; ++i) data[i]->ref = ref;
                        ref_tid = tid;
                }
                if (conf->flag & MPLP_GLF) {
@@ -680,7 +692,7 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.theta = 1e-3;
        mplp.min_baseQ = 13;
-       while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:u")) >= 0) {
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:t:Q:uaORH")) >= 0) {
                switch (c) {
                case 't': mplp.theta = atof(optarg); break;
                case 'f':
@@ -691,6 +703,10 @@ int bam_mpileup(int argc, char *argv[])
                case 'l': mplp.fn_pos = strdup(optarg); break;
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP; break;
+               case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN | MPLP_NO_HALFTRIM; break;
+               case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
+               case 'H': mplp.flag |= MPLP_NO_HALFTRIM; break;
+               case 'R': mplp.flag |= MPLP_REALN; 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;
@@ -706,7 +722,8 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -Q INT      min base quality [%d]\n", mplp.min_baseQ);
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -t FLOAT    scaled mutation rate [%lg]\n", mplp.theta);
-               fprintf(stderr, "         -g          generate GLF output\n");
+               fprintf(stderr, "         -g          generate BCF output\n");
+               fprintf(stderr, "         -u          do not compress BCF output\n");
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;