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;
+static float g_subsam = -1;
static char *g_library, *g_rg;
-static int g_sol2sanger_tbl[128];
static void *g_bed;
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 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];
- }
-}
-
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) {
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;
/* 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:L:")) >= 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;
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++;
}
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)
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;
+}
projects / samtools.git / blobdiff