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, is_count = 0;
+ 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 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:R:L:s:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 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(pysamerr, " -q INT minimum mapping quality [0]\n");
fprintf(pysamerr, " -l STR only output reads in library STR [null]\n");
fprintf(pysamerr, " -r STR only output reads in read group STR [null]\n");
- fprintf(pysamerr, " -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
fprintf(pysamerr, " -? longer help\n");
fprintf(pysamerr, "\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(pysamerr, "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;
-}