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[samtools.git] / bam_rmdup.c

diff --git a/bam_rmdup.c b/bam_rmdup.c
index 52ccd4cd1a70e982aec4de88da8941822e05354a..f0d2b5d54b462dac998f3cc094fdff1bbaac54bd 100644 (file)
--- a/bam_rmdup.c
+++ b/bam_rmdup.c
@@ -2,6 +2,7 @@
 #include <string.h>
 #include <stdio.h>
 #include <zlib.h>
+#include <unistd.h>
 #include "sam.h"
 
 typedef bam1_t *bam1_p;
@@ -32,11 +33,11 @@ static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
        stack->a[stack->n++] = b;
 }
 
-static inline void dump_best(tmp_stack_t *stack, bamFile out)
+static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
 {
        int i;
        for (i = 0; i != stack->n; ++i) {
-               bam_write1(out, stack->a[i]);
+               samwrite(out, stack->a[i]);
                bam_destroy1(stack->a[i]);
        }
        stack->n = 0;
@@ -86,9 +87,8 @@ static inline int sum_qual(const bam1_t *b)
        return q;
 }
 
-void bam_rmdup_core(bamFile in, bamFile out)
+void bam_rmdup_core(samfile_t *in, samfile_t *out)
 {
-       bam_header_t *header;
        bam1_t *b;
        int last_tid = -1, last_pos = -1;
        tmp_stack_t stack;
@@ -100,12 +100,9 @@ void bam_rmdup_core(bamFile in, bamFile out)
        del_set = kh_init(name);
        b = bam_init1();
        memset(&stack, 0, sizeof(tmp_stack_t));
-       header = bam_header_read(in);
-       sam_header_parse_rg(header);
-       bam_header_write(out, header);
 
        kh_resize(name, del_set, 4 * BUFFER_SIZE);
-       while (bam_read1(in, b) >= 0) {
+       while (samread(in, b) >= 0) {
                bam1_core_t *c = &b->core;
                if (c->tid != last_tid || last_pos != c->pos) {
                        dump_best(&stack, out); // write the result
@@ -117,24 +114,22 @@ void bam_rmdup_core(bamFile in, bamFile out)
                                        clear_del_set(del_set);
                                }
                                if ((int)c->tid == -1) { // append unmapped reads
-                                       bam_write1(out, b);
-                                       while (bam_read1(in, b) >= 0) bam_write1(out, b);
+                                       samwrite(out, b);
+                                       while (samread(in, b) >= 0) samwrite(out, b);
                                        break;
                                }
                                last_tid = c->tid;
-                               fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
+                               fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
                        }
                }
                if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
-                       bam_write1(out, b);
+                       samwrite(out, b);
                } else if (c->isize > 0) { // paired, head
                        uint64_t key = (uint64_t)c->pos<<32 | c->isize;
                        const char *lib;
-                       const uint8_t *rg;
                        lib_aux_t *q;
                        int ret;
-                       rg = bam_aux_get(b, "RG");
-                       lib = (rg == 0)? 0 : bam_strmap_get(header->rg2lib, (char*)(rg + 1));
+                       lib = bam_get_library(in->header, b);
                        q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
                        ++q->n_checked;
                        k = kh_put(pos, q->best_hash, key, &ret);
@@ -156,7 +151,7 @@ void bam_rmdup_core(bamFile in, bamFile out)
                        if (k != kh_end(del_set)) {
                                free((char*)kh_key(del_set, k));
                                kh_del(name, del_set, k);
-                       } else bam_write1(out, b);
+                       } else samwrite(out, b);
                }
                last_pos = c->pos;
        }
@@ -173,28 +168,39 @@ void bam_rmdup_core(bamFile in, bamFile out)
        }
        kh_destroy(lib, aux);
 
-       bam_header_destroy(header);
        clear_del_set(del_set);
        kh_destroy(name, del_set);
        free(stack.a);
        bam_destroy1(b);
 }
 
+void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);
+
 int bam_rmdup(int argc, char *argv[])
 {
-       bamFile in, out;
-       if (argc < 3) {
-               fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n");
+       int c, is_se = 0, force_se = 0;
+       samfile_t *in, *out;
+       while ((c = getopt(argc, argv, "sS")) >= 0) {
+               switch (c) {
+               case 's': is_se = 1; break;
+               case 'S': force_se = is_se = 1; break;
+               }
+       }
+       if (optind + 2 > argc) {
+               fprintf(stderr, "\n");
+               fprintf(stderr, "Usage:  samtools rmdup [-sS] <input.srt.bam> <output.bam>\n\n");
+               fprintf(stderr, "Option: -s    rmdup for SE reads\n");
+               fprintf(stderr, "        -S    treat PE reads as SE in rmdup (force -s)\n\n");
                return 1;
        }
-       in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
-       out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
+       in = samopen(argv[optind], "rb", 0);
+       out = samopen(argv[optind+1], "wb", in->header);
        if (in == 0 || out == 0) {
                fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
                return 1;
        }
-       bam_rmdup_core(in, out);
-       bam_close(in);
-       bam_close(out);
+       if (is_se) bam_rmdupse_core(in, out, force_se);
+       else bam_rmdup_core(in, out);
+       samclose(in); samclose(out);
        return 0;
 }