AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
- cut_target.o phase.o bam2depth.o
+ cut_target.o phase.o bam2depth.o padding.o
PROG= samtools
INCLUDES= -I.
SUBDIRS= . bcftools misc
/*! @abstract CIGAR: X = mismatch */
#define BAM_CDIFF 8
+#define BAM_CIGAR_STR "MIDNSHP=X"
+
+#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
+#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
+#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
+#define bam_cigar_gen(o, l) ((o)<<BAM_CIGAR_SHIFT|(l))
+
/*! @typedef
@abstract Structure for core alignment information.
@field tid chromosome ID, defined by bam_header_t
#include <stdlib.h>
#include <string.h>
+#include "kstring.h"
#include "bam.h"
+void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
+{
+ bam1_t *swap;
+ int i, end;
+ uint32_t *cigar;
+ str->l = 0;
+ if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
+ if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
+ kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+ kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+ for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
+ kputw(bam_cigar_oplen(cigar[i]), str);
+ kputc(bam_cigar_opchr(cigar[i]), str);
+ }
+ end = bam_calend(&b1->core, cigar);
+ kputw(b2->core.pos - end, str);
+ kputc('T', str);
+ kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+ kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+ for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
+ kputw(bam_cigar_oplen(cigar[i]), str);
+ kputc(bam_cigar_opchr(cigar[i]), str);
+ }
+ bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s);
+}
+
// currently, this function ONLY works if each read has one hit
void bam_mating_core(bamFile in, bamFile out)
{
bam_header_t *header;
bam1_t *b[2];
- int curr, has_prev;
+ int curr, has_prev, pre_end, cur_end;
+ kstring_t str;
+ str.l = str.m = 0; str.s = 0;
header = bam_header_read(in);
bam_header_write(out, header);
curr = 0; has_prev = 0;
while (bam_read1(in, b[curr]) >= 0) {
bam1_t *cur = b[curr], *pre = b[1-curr];
+ if (cur->core.tid < 0) continue;
+ cur_end = bam_calend(&cur->core, bam1_cigar(cur));
+ if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
+ if (cur->core.flag & BAM_FSECONDARY) continue; // skip secondary alignments
if (has_prev) {
if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
- && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
+ && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
{
uint32_t cur5, pre5;
- cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
- pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
+ cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
+ pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
} else cur->core.isize = pre->core.isize = 0;
if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
else pre->core.flag &= ~BAM_FMREVERSE;
if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
+ bam_template_cigar(pre, cur, &str);
bam_write1(out, pre);
bam_write1(out, cur);
has_prev = 0;
}
} else has_prev = 1;
curr = 1 - curr;
+ pre_end = cur_end;
}
if (has_prev) bam_write1(out, b[1-curr]);
bam_header_destroy(header);
bam_destroy1(b[0]);
bam_destroy1(b[1]);
+ free(str.s);
}
int bam_mating(int argc, char *argv[])
{
bamFile in, out;
if (argc < 3) {
- fprintf(stderr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+ fprintf(stderr, "Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
return 1;
}
in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
int main_cat(int argc, char *argv[]);
int main_depth(int argc, char *argv[]);
int main_bam2fq(int argc, char *argv[]);
+int main_pad2unpad(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
fprintf(stderr, " cat concatenate BAMs\n");
fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
fprintf(stderr, " phase phase heterozygotes\n");
+ fprintf(stderr, " pad2unpad convert padded BAM to unpadded BAM\n");
fprintf(stderr, "\n");
#ifdef _WIN32
fprintf(stderr, "\
else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+ else if (strcmp(argv[1], "pad2unpad") == 0) return main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) {
fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
static int *ksBM_prep(const ubyte_t *pat, int m)
{
int i, *suff, *prep, *bmGs, *bmBc;
- prep = calloc(m + 256, sizeof(int));
+ prep = (int*)calloc(m + 256, sizeof(int));
bmGs = prep; bmBc = prep + m;
{ // preBmBc()
for (i = 0; i < 256; ++i) bmBc[i] = m;
for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
}
- suff = calloc(m, sizeof(int));
+ suff = (int*)calloc(m, sizeof(int));
{ // suffixes()
int f = 0, g;
suff[m - 1] = m;
+/* The MIT License
+
+ Copyright (c) by Attractive Chaos <attractor@live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
#ifndef KSTRING_H
#define KSTRING_H
#ifdef __cplusplus
}
#endif
-
+
+static inline void ks_resize(kstring_t *s, size_t size)
+{
+ if (s->m < size) {
+ s->m = size;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+}
+
static inline int kputsn(const char *p, int l, kstring_t *s)
{
if (s->l + l + 1 >= s->m) {
--- /dev/null
+#include <string.h>
+#include <assert.h>
+#include "kstring.h"
+#include "bam.h"
+
+static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
+{
+ if (n != b->core.n_cigar) {
+ int o = b->core.l_qname + b->core.n_cigar * 4;
+ if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
+ b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
+ memcpy(b->data + b->core.l_qname, cigar, n * 4);
+ b->data_len += (n - b->core.n_cigar) * 4;
+ b->core.n_cigar = n;
+ } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
+}
+
+#define write_cigar(_c, _n, _m, _v) do { \
+ if (_n == _m) { \
+ _m = _m? _m<<1 : 4; \
+ _c = (uint32_t*)realloc(_c, _m * 4); \
+ } \
+ _c[_n++] = (_v); \
+ } while (0)
+
+static void unpad_seq(bam1_t *b, kstring_t *s)
+{
+ int k, j, i;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *seq = bam1_seq(b);
+ ks_resize(s, b->core.l_qseq);
+ for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
+ int op, ol;
+ op = bam_cigar_op(cigar[k]);
+ ol = bam_cigar_oplen(cigar[k]);
+ assert(op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CSOFT_CLIP);
+ if (op == BAM_CMATCH) {
+ for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
+ ++j;
+ } else if (op == BAM_CSOFT_CLIP) {
+ j += ol;
+ } else {
+ for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+ }
+ }
+}
+
+int bam_pad2unpad(bamFile in, bamFile out)
+{
+ bam_header_t *h;
+ bam1_t *b;
+ kstring_t r, q;
+ uint32_t *cigar2 = 0;
+ int n2 = 0, m2 = 0, *posmap = 0;
+
+ h = bam_header_read(in);
+ bam_header_write(out, h);
+ b = bam_init1();
+ r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
+ while (bam_read1(in, b) >= 0) {
+ uint32_t *cigar = bam1_cigar(b);
+ n2 = 0;
+ if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
+ int i, k;
+ unpad_seq(b, &r);
+ write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
+ replace_cigar(b, n2, cigar2);
+ posmap = realloc(posmap, r.m * sizeof(int));
+ for (i = k = 0; i < r.l; ++i) {
+ posmap[i] = k; // note that a read should NOT start at a padding
+ if (r.s[i]) ++k;
+ }
+ } else {
+ int i, k, op;
+ unpad_seq(b, &q);
+ if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
+ q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+ for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
+ if (op != q.s[i]) {
+ write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+ op = q.s[i]; k = 1;
+ } else ++k;
+ }
+ write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+ if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ for (i = 2; i < n2; ++i)
+ if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
+ cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
+ for (i = k = 0; i < n2; ++i)
+ if (cigar2[i]) cigar2[k++] = cigar2[i];
+ n2 = k;
+ replace_cigar(b, n2, cigar2);
+ b->core.pos = posmap[b->core.pos];
+ }
+ bam_write1(out, b);
+ }
+ free(r.s); free(q.s); free(posmap);
+ bam_destroy1(b);
+ bam_header_destroy(h);
+ return 0;
+}
+
+int main_pad2unpad(int argc, char *argv[])
+{
+ bamFile in, out;
+ if (argc == 1) {
+ fprintf(stderr, "Usage: samtools pad2unpad <in.bam>\n");
+ return 1;
+ }
+ in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+ out = bam_dopen(fileno(stdout), "w");
+ bam_pad2unpad(in, out);
+ bam_close(in); bam_close(out);
+ return 0;
+}
projects / samtools.git / commitdiff