works

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index b6896c908cb367c1083eb3fbe994fe3c83a753f4..528309897bbf7c2a35bb4f2fa4727f522afb889e 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -14,15 +14,16 @@ KHASH_SET_INIT_STR(rg)
 // data passed to the bam_fetch callback is encapsulated in this struct.
 typedef struct {
        bam_header_t *header;
-       int *count;
+       int64_t *count;  // int does overflow for very big BAMs
 } count_func_data_t;
 
 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, g_qual_scale = 0;
-static float g_subsam = -1;
+static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0, g_min_qlen = 0;
+static uint32_t g_subsam_seed = 0;
+static double g_subsam_frac = -1.;
 static char *g_library, *g_rg;
 static void *g_bed;
 
@@ -40,14 +41,21 @@ static int process_aln(const bam_header_t *h, bam1_t *b)
                        qual[i] = c < 93? c : 93;
                }
        }
+       if (g_min_qlen > 0) {
+               int k, qlen = 0;
+               uint32_t *cigar = bam1_cigar(b);
+               for (k = 0; k < b->core.n_cigar; ++k)
+                       if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
+                               qlen += bam_cigar_oplen(cigar[k]);
+               if (qlen < g_min_qlen) return 1;
+       }
        if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
                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.) {
-               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_subsam_frac > 0.) {
+               uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + g_subsam_seed;
+               if ((double)(k&0xffffff) / 0x1000000 >= g_subsam_frac) return 1;
        }
        if (g_rg || g_rghash) {
                uint8_t *s = bam_aux_get(b, "RG");
@@ -120,15 +128,22 @@ int main_samview(int argc, char *argv[])
 {
        int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
        int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
-       int count = 0;
+       int64_t count = 0;
        samfile_t *in = 0, *out = 0;
-       char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
+       char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:")) >= 0) {
+       while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:m:")) >= 0) {
                switch (c) {
-               case 's': g_subsam = atof(optarg); break;
+               case 's':
+                       if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
+                               srand(g_subsam_seed);
+                               g_subsam_seed = rand();
+                       }
+                       g_subsam_frac = strtod(q, &q);
+                       break;
+               case 'm': g_min_qlen = atoi(optarg); break;
                case 'c': is_count = 1; break;
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
@@ -259,7 +274,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
        if (is_count && ret == 0) {
-               printf("%d\n", count);
+               printf("%ld\n", count); // compilers on some platforms may complain about printing int64_t with %ld
        }
        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
@@ -361,12 +376,14 @@ int main_bam2fq(int argc, char *argv[])
        bam_header_t *h;
        bam1_t *b;
        int8_t *buf;
-       int max_buf;
+       int max_buf, c, no12 = 0;
+       while ((c = getopt(argc, argv, "n")) > 0)
+               if (c == 'n') no12 = 1;
        if (argc == 1) {
                fprintf(stderr, "Usage: samtools bam2fq <in.bam>\n");
                return 1;
        }
-       fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+       fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
        if (fp == 0) return 1;
        h = bam_header_read(fp);
        b = bam_init1();
@@ -376,9 +393,12 @@ int main_bam2fq(int argc, char *argv[])
                int i, qlen = b->core.l_qseq;
                uint8_t *seq;
                putchar('@'); fputs(bam1_qname(b), stdout);
-               if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
-               else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
-               else putchar('\n');
+               if (no12) putchar('\n');
+               else {
+                       if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
+                       else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
+                       else putchar('\n');
+               }
                if (max_buf < qlen + 1) {
                        max_buf = qlen + 1;
                        kroundup32(max_buf);