allow to set seed in view-subsampling

diff --git a/sam_view.c b/sam_view.c
index ad74962cbb603884a4b8f97a0669d073f31de550..efda4e8b93cef37a1a354724695b039bfbf0017f 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -22,7 +22,7 @@ typedef khash_t(rg) *rghash_t;
 // FIXME: we'd better use no global variables...
 static rghash_t g_rghash = 0;
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
-static float g_subsam = 2.;
+static float g_subsam = -1;
 static char *g_library, *g_rg;
 static void *g_bed;
 
@@ -36,9 +36,10 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
                return 1;
        if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
                return 1;
-       if (g_subsam > 0. && g_subsam < 1.) {
-               uint32_t k = __ac_X31_hash_string(bam1_qname(b));
-               if (k%1024 / 1024.0 >= g_subsam) return 1;
+       if (g_subsam > 0.) {
+               int x = (int)(g_subsam + .499);
+               uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
+               if (k%1024 / 1024.0 >= g_subsam - x) return 1;
        }
        if (g_rg || g_rghash) {
                uint8_t *s = bam_aux_get(b, "RG");
@@ -286,7 +287,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -q INT   minimum mapping quality [0]\n");
        fprintf(stderr, "         -l STR   only output reads in library STR [null]\n");
        fprintf(stderr, "         -r STR   only output reads in read group STR [null]\n");
-       fprintf(stderr, "         -s FLOAT fraction of templates (read paris) to subsample [1]\n");
+       fprintf(stderr, "         -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
        fprintf(stderr, "         -?       longer help\n");
        fprintf(stderr, "\n");
        if (is_long_help)