X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=sam_view.c;h=efda4e8b93cef37a1a354724695b039bfbf0017f;hp=170bd843608b99aec35161141ee6afaad848db5e;hb=HEAD;hpb=6828a9a9ef02c5634d488a3b3a52966a92d38088 diff --git a/sam_view.c b/sam_view.c index 170bd84..efda4e8 100644 --- a/sam_view.c +++ b/sam_view.c @@ -6,6 +6,7 @@ #include "sam_header.h" #include "sam.h" #include "faidx.h" +#include "kstring.h" #include "khash.h" KHASH_SET_INIT_STR(rg) @@ -18,32 +19,28 @@ typedef struct { 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 float g_subsam = -1; 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; + 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) { @@ -61,6 +58,37 @@ static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b) return 0; } +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) { @@ -82,7 +110,7 @@ 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, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 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 count = 0; samfile_t *in = 0, *out = 0; @@ -90,10 +118,10 @@ int main_samview(int argc, char *argv[]) /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); - while ((c = getopt(argc, argv, "Sbct:h1Ho: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) { + case 's': g_subsam = atof(optarg); break; case 'c': is_count = 1; break; - case 'C': slx2sngr = 1; break; case 'S': is_bamin = 0; break; case 'b': is_bamout = 1; break; case 't': fn_list = strdup(optarg); is_bamin = 0; break; @@ -106,6 +134,7 @@ int main_samview(int argc, char *argv[]) case 'u': compress_level = 0; break; case '1': compress_level = 1; 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; @@ -156,6 +185,14 @@ int main_samview(int argc, char *argv[]) ret = 1; goto view_end; } + 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; @@ -168,7 +205,6 @@ 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)) { - if (slx2sngr) sol2sanger(b); if (!is_count) samwrite(out, b); // write the alignment to `out' count++; } @@ -215,6 +251,7 @@ view_end: } // 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) @@ -240,6 +277,7 @@ static int usage(int is_long_help) 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"); @@ -249,6 +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, " -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) @@ -299,3 +338,69 @@ int main_import(int argc, char *argv[]) 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 \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; +}