Fix missing declaration for getopt on Mac OS X

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index d1178ffd4dd36c8805ef00230c51ff161af226c6..c7a47747b4aba916911534591411ae0721b962a2 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -21,7 +21,7 @@ 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, g_qual_scale = 0;
+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;
@@ -41,6 +41,14 @@ 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))))
@@ -126,7 +134,7 @@ int main_samview(int argc, char *argv[])
 
        /* 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':
                        if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
@@ -135,6 +143,7 @@ int main_samview(int argc, char *argv[])
                        }
                        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;
@@ -367,12 +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();
@@ -382,9 +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);