Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt...

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index 3b10e2e5372e98a2b9ebda4bd5791dc1b837a20f..efda4e8b93cef37a1a354724695b039bfbf0017f 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -6,37 +6,41 @@
 #include "sam_header.h"
 #include "sam.h"
 #include "faidx.h"
 #include "sam_header.h"
 #include "sam.h"
 #include "faidx.h"

+#include "kstring.h"

 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 
 #include "khash.h"
 KHASH_SET_INIT_STR(rg)
 

+// When counting records instead of printing them,
+// data passed to the bam_fetch callback is encapsulated in this struct.
+typedef struct {
+       bam_header_t *header;
+       int *count;
+} count_func_data_t;
+

 typedef khash_t(rg) *rghash_t;
 
 typedef khash_t(rg) *rghash_t;
 

-rghash_t g_rghash = 0;
+// 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 int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;

+static float g_subsam = -1;

 static char *g_library, *g_rg;
 static char *g_library, *g_rg;

-static int g_sol2sanger_tbl[128];
+static void *g_bed;

 
 

-static void sol2sanger(bam1_t *b)
-{
-       int l;
-       uint8_t *qual = bam1_qual(b);
-       if (g_sol2sanger_tbl[30] == 0) {
-               for (l = 0; l != 128; ++l) {
-                       g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
-                       if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
-               }
-       }
-       for (l = 0; l < b->core.l_qseq; ++l) {
-               int q = qual[l];
-               if (q > 127) q = 127;
-               qual[l] = g_sol2sanger_tbl[q];
-       }
-}
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);

 
 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
        if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
                return 1;
 
 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
        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_rg || g_rghash) {
                uint8_t *s = bam_aux_get(b, "RG");
                if (s) {
        if (g_rg || g_rghash) {
                uint8_t *s = bam_aux_get(b, "RG");
                if (s) {


@@ -54,7 +58,38 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
        return 0;
 }
 
        return 0;
 }
 

-// callback function for bam_fetch()
+static char *drop_rg(char *hdtxt, rghash_t h, int *len)
+{
+       char *p = hdtxt, *q, *r, *s;
+       kstring_t str;
+       memset(&str, 0, sizeof(kstring_t));
+       while (1) {
+               int toprint = 0;
+               q = strchr(p, '\n');
+               if (q == 0) q = p + strlen(p);
+               if (q - p < 3) break; // the line is too short; then stop
+               if (strncmp(p, "@RG\t", 4) == 0) {
+                       int c;
+                       khint_t k;
+                       if ((r = strstr(p, "\tID:")) != 0) {
+                               r += 4;
+                               for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
+                               c = *s; *s = '\0';
+                               k = kh_get(rg, h, r);
+                               *s = c;
+                               if (k != kh_end(h)) toprint = 1;
+                       }
+               } else toprint = 1;
+               if (toprint) {
+                       kputsn(p, q - p, &str); kputc('\n', &str);
+               }
+               p = q + 1;
+       }
+       *len = str.l;
+       return str.s;
+}
+
+// callback function for bam_fetch() that prints nonskipped records

 static int view_func(const bam1_t *b, void *data)
 {
        if (!__g_skip_aln(((samfile_t*)data)->header, b))
 static int view_func(const bam1_t *b, void *data)
 {
        if (!__g_skip_aln(((samfile_t*)data)->header, b))


@@ -62,20 +97,31 @@ static int view_func(const bam1_t *b, void *data)
        return 0;
 }
 
        return 0;
 }
 

+// callback function for bam_fetch() that counts nonskipped records
+static int count_func(const bam1_t *b, void *data)
+{
+       if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+               (*((count_func_data_t*)data)->count)++;
+       }
+       return 0;
+}
+

 static int usage(int is_long_help);
 
 int main_samview(int argc, char *argv[])
 {
 static int usage(int is_long_help);
 
 int main_samview(int argc, char *argv[])
 {

-       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0;
+       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;
        int of_type = BAM_OFDEC, is_long_help = 0;

+       int 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;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
        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;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");

-       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:")) >= 0) {

                switch (c) {
                switch (c) {

-               case 'C': slx2sngr = 1; break;
+               case 's': g_subsam = atof(optarg); break;
+               case 'c': is_count = 1; break;

                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
                case 't': fn_list = strdup(optarg); is_bamin = 0; break;
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
                case 't': fn_list = strdup(optarg); is_bamin = 0; break;


@@ -85,8 +131,10 @@ int main_samview(int argc, char *argv[])
                case 'f': g_flag_on = strtol(optarg, 0, 0); break;
                case 'F': g_flag_off = strtol(optarg, 0, 0); break;
                case 'q': g_min_mapQ = atoi(optarg); break;
                case 'f': g_flag_on = strtol(optarg, 0, 0); break;
                case 'F': g_flag_off = strtol(optarg, 0, 0); break;
                case 'q': g_min_mapQ = atoi(optarg); break;

-               case 'u': is_uncompressed = 1; break;
+               case 'u': compress_level = 0; break;
+               case '1': compress_level = 1; break;

                case 'l': g_library = strdup(optarg); break;
                case 'l': g_library = strdup(optarg); break;

+               case 'L': g_bed = bed_read(optarg); break;

                case 'r': g_rg = strdup(optarg); break;
                case 'R': fn_rg = strdup(optarg); break;
                case 'x': of_type = BAM_OFHEX; break;
                case 'r': g_rg = strdup(optarg); break;
                case 'R': fn_rg = strdup(optarg); break;
                case 'x': of_type = BAM_OFHEX; break;


@@ -96,7 +144,7 @@ int main_samview(int argc, char *argv[])
                default: return usage(is_long_help);
                }
        }
                default: return usage(is_long_help);
                }
        }

-       if (is_uncompressed) is_bamout = 1;
+       if (compress_level >= 0) is_bamout = 1;

        if (is_header_only) is_header = 1;
        if (is_bamout) strcat(out_mode, "b");
        else {
        if (is_header_only) is_header = 1;
        if (is_bamout) strcat(out_mode, "b");
        else {


@@ -105,7 +153,11 @@ int main_samview(int argc, char *argv[])
        }
        if (is_bamin) strcat(in_mode, "b");
        if (is_header) strcat(out_mode, "h");
        }
        if (is_bamin) strcat(in_mode, "b");
        if (is_header) strcat(out_mode, "h");

-       if (is_uncompressed) strcat(out_mode, "u");
+       if (compress_level >= 0) {
+               char tmp[2];
+               tmp[0] = compress_level + '0'; tmp[1] = '\0';
+               strcat(out_mode, tmp);
+       }

        if (argc == optind) return usage(is_long_help); // potential memory leak...
 
        // read the list of read groups
        if (argc == optind) return usage(is_long_help); // potential memory leak...
 
        // read the list of read groups


@@ -124,15 +176,26 @@ int main_samview(int argc, char *argv[])
        if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
        // open file handlers
        if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
        if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
        // open file handlers
        if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {

-               fprintf(stderr, "[main_samview] fail to open file for reading.\n");
+               fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
+               ret = 1;

                goto view_end;
        }
        if (in->header == 0) {
                goto view_end;
        }
        if (in->header == 0) {

-               fprintf(stderr, "[main_samview] fail to read the header.\n");
+               fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
+               ret = 1;

                goto view_end;
        }
                goto view_end;
        }

-       if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
-               fprintf(stderr, "[main_samview] fail to open file for writing.\n");
+       if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
+               char *tmp;
+               int l;
+               tmp = drop_rg(in->header->text, g_rghash, &l);
+               free(in->header->text);
+               in->header->text = tmp;
+               in->header->l_text = l;
+       }
+       if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+               fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+               ret = 1;

                goto view_end;
        }
        if (is_header_only) goto view_end; // no need to print alignments
                goto view_end;
        }
        if (is_header_only) goto view_end; // no need to print alignments


@@ -142,11 +205,14 @@ int main_samview(int argc, char *argv[])
                int r;
                while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
                        if (!__g_skip_aln(in->header, b)) {
                int r;
                while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
                        if (!__g_skip_aln(in->header, b)) {

-                               if (slx2sngr) sol2sanger(b);
-                               samwrite(out, b); // write the alignment to `out'
+                               if (!is_count) samwrite(out, b); // write the alignment to `out'
+                               count++;

                        }
                }
                        }
                }

-               if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
+               if (r < -1) {
+                       fprintf(stderr, "[main_samview] truncated file.\n");
+                       ret = 1;
+               }

                bam_destroy1(b);
        } else { // retrieve alignments in specified regions
                int i;
                bam_destroy1(b);
        } else { // retrieve alignments in specified regions
                int i;


@@ -158,20 +224,34 @@ int main_samview(int argc, char *argv[])
                        goto view_end;
                }
                for (i = optind + 1; i < argc; ++i) {
                        goto view_end;
                }
                for (i = optind + 1; i < argc; ++i) {

-                       int tid, beg, end;
+                       int tid, beg, end, result;

                        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
                        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");
+                               fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);

                                continue;
                        }
                                continue;
                        }

-                       bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments
+                       // fetch alignments
+                       if (is_count) {
+                               count_func_data_t count_data = { in->header, &count };
+                               result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
+                       } else
+                               result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
+                       if (result < 0) {
+                               fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
+                               ret = 1;
+                               break;
+                       }

                }
                bam_index_destroy(idx); // destroy the BAM index
        }
 
 view_end:
                }
                bam_index_destroy(idx); // destroy the BAM index
        }
 
 view_end:

+       if (is_count && ret == 0) {
+               printf("%d\n", count);
+       }

        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
        // close files, free and return
        free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);

+       if (g_bed) bed_destroy(g_bed);

        if (g_rghash) {
                khint_t k;
                for (k = 0; k < kh_end(g_rghash); ++k)
        if (g_rghash) {
                khint_t k;
                for (k = 0; k < kh_end(g_rghash); ++k)


@@ -179,7 +259,8 @@ view_end:
                kh_destroy(rg, g_rghash);
        }
        samclose(in);
                kh_destroy(rg, g_rghash);
        }
        samclose(in);

-       samclose(out);
+       if (!is_count)
+               samclose(out);

        return ret;
 }
 
        return ret;
 }
 


@@ -192,8 +273,11 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -H       print header only (no alignments)\n");
        fprintf(stderr, "         -S       input is SAM\n");
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
        fprintf(stderr, "         -H       print header only (no alignments)\n");
        fprintf(stderr, "         -S       input is SAM\n");
        fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");

+       fprintf(stderr, "         -1       fast compression (force -b)\n");

        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
        fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
        fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");

+       fprintf(stderr, "         -c       print only the count of matching records\n");
+       fprintf(stderr, "         -L FILE  output alignments overlapping the input BED FILE [null]\n");

        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");
        fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");


@@ -203,6 +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, "         -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 to subsample; integer part as seed [-1]\n");

        fprintf(stderr, "         -?       longer help\n");
        fprintf(stderr, "\n");
        if (is_long_help)
        fprintf(stderr, "         -?       longer help\n");
        fprintf(stderr, "\n");
        if (is_long_help)


@@ -253,3 +338,69 @@ int main_import(int argc, char *argv[])
        free(argv2);
        return ret;
 }
        free(argv2);
        return ret;
 }

+
+int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };
+
+int main_bam2fq(int argc, char *argv[])
+{
+       bamFile fp;
+       bam_header_t *h;
+       bam1_t *b;
+       int8_t *buf;
+       int max_buf;
+       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");
+       if (fp == 0) return 1;
+       h = bam_header_read(fp);
+       b = bam_init1();
+       buf = 0;
+       max_buf = 0;
+       while (bam_read1(fp, b) >= 0) {
+               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 (max_buf < qlen + 1) {
+                       max_buf = qlen + 1;
+                       kroundup32(max_buf);
+                       buf = realloc(buf, max_buf);
+               }
+               buf[qlen] = 0;
+               seq = bam1_seq(b);
+               for (i = 0; i < qlen; ++i)
+                       buf[i] = bam1_seqi(seq, i);
+               if (b->core.flag & 16) { // reverse complement
+                       for (i = 0; i < qlen>>1; ++i) {
+                               int8_t t = seq_comp_table[buf[qlen - 1 - i]];
+                               buf[qlen - 1 - i] = seq_comp_table[buf[i]];
+                               buf[i] = t;
+                       }
+                       if (qlen&1) buf[i] = seq_comp_table[buf[i]];
+               }
+               for (i = 0; i < qlen; ++i)
+                       buf[i] = bam_nt16_rev_table[buf[i]];
+               puts((char*)buf);
+               puts("+");
+               seq = bam1_qual(b);
+               for (i = 0; i < qlen; ++i)
+                       buf[i] = 33 + seq[i];
+               if (b->core.flag & 16) { // reverse
+                       for (i = 0; i < qlen>>1; ++i) {
+                               int8_t t = buf[qlen - 1 - i];
+                               buf[qlen - 1 - i] = buf[i];
+                               buf[i] = t;
+                       }
+               }
+               puts((char*)buf);
+       }
+       free(buf);
+       bam_destroy1(b);
+       bam_header_destroy(h);
+       bam_close(fp);
+       return 0;
+}