+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include "sam.h"
+
+static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
+
+// callback function for bam_fetch()
+static int view_func(const bam1_t *b, void *data)
+{
+ if (b->core.qual < g_min_mapQ) return 0;
+ if (g_flag_on && (b->core.flag & g_flag_on) == 0) return 0;
+ if (b->core.flag & g_flag_off) return 0;
+ samwrite((samfile_t*)data, b);
+ return 0;
+}
+
+static int usage(void);
+
+int main_samview(int argc, char *argv[])
+{
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0;
+ samfile_t *in, *out;
+ char in_mode[4], out_mode[4], *fn_out = 0, *fn_list = 0;
+
+ /* parse command-line options */
+ strcpy(in_mode, "r"); strcpy(out_mode, "w");
+ while ((c = getopt(argc, argv, "bt:hHo:q:f:F:")) >= 0) {
+ switch (c) {
+ case 'b': strcat(out_mode, "b"); break;
+ case 't': fn_list = strdup(optarg); is_bamin = 0; break;
+ case 'h': is_header = 1; break;
+ case 'H': is_header_only = 1; break;
+ case 'o': fn_out = strdup(optarg); break;
+ case 'f': g_flag_on = strtol(optarg, 0, 0); break;
+ case 'F': g_flag_on = strtol(optarg, 0, 0); break;
+ case 'q': g_min_mapQ = atoi(optarg); break;
+ default: return usage();
+ }
+ }
+ if (is_header_only) is_header = 1;
+ if (is_bamin) strcat(in_mode, "b");
+ if (is_header) strcat(out_mode, "h");
+ if (argc == optind) return usage();
+
+ // open file handlers
+ in = samopen(argv[optind], in_mode, fn_list);
+ out = samopen(fn_out? fn_out : "-", out_mode, in->header);
+ if (is_header_only) goto view_end; // no need to print alignments
+
+ if (argc == optind + 1) { // convert/print the entire file
+ bam1_t *b = bam_init1();
+ int r;
+ while ((r = samread(in, b)) >= 0) // read one alignment from `in'
+ samwrite(out, b); // write the alignment to `out'
+ if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
+ bam_destroy1(b);
+ } else { // retrieve alignments in specified regions
+ int i;
+ bam_index_t *idx = 0;
+ if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
+ if (idx == 0) { // index is unavailable
+ fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
+ ret = 1;
+ goto view_end;
+ }
+ for (i = optind + 1; i < argc; ++i) {
+ int tid, beg, end;
+ bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
+ if (tid < 0) { // reference name is not found
+ fprintf(stderr, "[main_samview] fail to get the reference name. Continue anyway.\n");
+ continue;
+ }
+ bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
+ }
+ bam_index_destroy(idx); // destroy the BAM index
+ }
+
+view_end:
+ // close files, free and return
+ free(fn_list); free(fn_out);
+ samclose(in);
+ samclose(out);
+ return ret;
+}
+
+static int usage()
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n");
+ fprintf(stderr, "Options: -b output BAM\n");
+ fprintf(stderr, " -h print header for the SAM output\n");
+ fprintf(stderr, " -H print header only (no alignments)\n");
+ fprintf(stderr, " -t FILE list of reference names and lengths, assuming SAM input [null]\n");
+ fprintf(stderr, " -o FILE output file name [stdout]\n");
+ fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");
+ fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n");
+ fprintf(stderr, " -q INT minimum mapping quality [0]\n");
+ fprintf(stderr, "\n\
+Notes:\n\
+\n\
+ 1. By default, this command assumes the file on the command line is in\n\
+ the BAM format and it prints the alignments in SAM. If `-t' is\n\
+ applied, the input file is assumed to be in the SAM format. The\n\
+ file supplied with `-t' is SPACE/TAB delimited with the first two\n\
+ fields of each line consisting of the reference name and the\n\
+ corresponding sequence length. The `.fai' file generated by `faidx'\n\
+ can be used here. This file may be empty if reads are unaligned.\n\
+\n\
+ 2. SAM->BAM conversion: `samtools view -bt ref.fa.fai in.sam.gz'.\n\
+\n\
+ 3. BAM->SAM conversion: `samtools view in.bam'.\n\
+\n\
+ 4. A region should be presented in one of the following formats:\n\
+ `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
+ specified, the input alignment file must be an indexed BAM file.\n\
+\n");
+ return 1;
+}
+
+int main_import(int argc, char *argv[])
+{
+ int argc2, ret;
+ char **argv2;
+ if (argc != 4) {
+ fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n");
+ return 1;
+ }
+ argc2 = 6;
+ argv2 = calloc(6, sizeof(char*));
+ argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
+ ret = main_samview(argc2, argv2);
+ free(argv2);
+ return ret;
+}