* samtools-0.1.8-20 (r778)

 * speed up pileup, although I do not know how much is the improvement

diff --git a/bam.h b/bam.h
index a8769e26a38c3dc62ee4ded2dc793a90884d19a3..5943123d608ddca0b9bbee08741101fe9a5f0cb7 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -495,7 +495,7 @@ extern "C" {
                bam1_t *b;
                int32_t qpos;
                int indel, level;
-               uint32_t is_del:1, is_head:1, is_tail:1;
+               uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1;
        } bam_pileup1_t;
 
        typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);

diff --git a/bam_pileup.c b/bam_pileup.c
index 266b96673713e3800001624bbf0f0a3baed78637..62d5fa1d2b3d9b2171b98eccb9f583755e379822 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -4,9 +4,16 @@
 #include <assert.h>
 #include "sam.h"
 
+typedef struct {
+       int k, x, y, end;
+} cstate_t;
+
+static cstate_t g_cstate_null = { -1, 0, 0, 0 };
+
 typedef struct __linkbuf_t {
        bam1_t b;
        uint32_t beg, end;
+       cstate_t s;
        struct __linkbuf_t *next;
 } lbnode_t;
 
@@ -53,72 +60,83 @@ static inline void mp_free(mempool_t *mp, lbnode_t *p)
 
 /* --- BEGIN: Auxiliary functions */
 
-static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
+/* s->k: the index of the CIGAR operator that has just been processed.
+   s->x: the reference coordinate of the start of s->k
+   s->y: the query coordiante of the start of s->k
+ */
+static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
 {
-       unsigned k;
+#define _cop(c) ((c)&BAM_CIGAR_MASK)
+#define _cln(c) ((c)>>BAM_CIGAR_SHIFT)
+
        bam1_t *b = p->b;
        bam1_core_t *c = &b->core;
-       uint32_t x = c->pos, y = 0;
-       int ret = 1, is_restart = 1, first_op, last_op;
-
-       if (c->flag&BAM_FUNMAP) return 0; // unmapped read
-       assert(x <= pos); // otherwise a bug
-       p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
-       first_op = bam1_cigar(b)[0] & BAM_CIGAR_MASK;
-       last_op = bam1_cigar(b)[c->n_cigar-1] & BAM_CIGAR_MASK;
-       for (k = 0; k < c->n_cigar; ++k) {
-               int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
-               int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
-               if (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip
-                       if (x + l > pos) { // overlap with pos
-                               p->indel = p->is_del = 0;
-                               p->qpos = y + (pos - x);
-                               if (x == pos && is_restart && first_op != BAM_CDEL) p->is_head = 1;
-                               if (x + l - 1 == pos) { // come to the end of a match
-                                       int has_next_match = 0;
-                                       unsigned i;
-                                       for (i = k + 1; i < c->n_cigar; ++i) {
-                                               uint32_t cigar = bam1_cigar(b)[i];
-                                               int opi = cigar&BAM_CIGAR_MASK;
-                                               if (opi == BAM_CMATCH) {
-                                                       has_next_match = 1;
-                                                       break;
-                                               } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
-                                       }
-                                       if (!has_next_match && last_op != BAM_CDEL) p->is_tail = 1;
-                                       if (k < c->n_cigar - 1 && has_next_match) { // there are additional operation(s)
-                                               uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
-                                               int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
-                                               if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
-                                               else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
-                                               else if (op_next == BAM_CPAD && k + 2 < c->n_cigar) { // no working for adjacent padding
-                                                       cigar = bam1_cigar(b)[k+2]; op_next = cigar&BAM_CIGAR_MASK;
-                                                       if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
-                                                       else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
-                                               }
-                                       }
+       uint32_t *cigar = bam1_cigar(b);
+       int k, is_head = 0;
+       // determine the current CIGAR operation
+//     fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y);
+       if (s->k == -1) { // never processed
+               is_head = 1;
+               if (c->n_cigar == 1) { // just one operation, save a loop
+                       if (_cop(cigar[0]) == BAM_CMATCH) s->k = 0, s->x = c->pos, s->y = 0;
+               } else { // find the first match
+                       for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
+                               int op = _cop(cigar[k]);
+                               int l = _cln(cigar[k]);
+                               if (op == BAM_CMATCH) break;
+                               else if (op == BAM_CDEL || op == BAM_CREF_SKIP) s->x += l;
+                               else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
+                       }
+                       assert(k < c->n_cigar);
+                       s->k = k;
+               }
+       } else { // the read has been processed before
+               int op, l = _cln(cigar[s->k]);
+               if (pos - s->x >= l) { // jump to the next operation
+                       assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
+                       op = _cop(cigar[s->k+1]);
+                       if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) { // jump to the next without a loop
+                               if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
+                               s->x += l;
+                               ++s->k;
+                       } else { // find the next M/D/N
+                               if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
+                               s->x += l;
+                               for (k = s->k + 1; k < c->n_cigar; ++k) {
+                                       op = _cop(cigar[k]), l = _cln(cigar[k]);
+                                       if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) break;
+                                       else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
                                }
+                               s->k = k;
                        }
-                       x += l; y += l;
-               } else if (op == BAM_CDEL) { // then set ->is_del
-                       if (k == 0 && x == pos) p->is_head = 1;
-                       else if (x + l - 1 == pos && k == c->n_cigar - 1) p->is_tail = 1;
-                       if (x + l > pos) {
-                               p->indel = 0; p->is_del = 1;
-                               p->qpos = y;
+                       assert(s->k < c->n_cigar); // otherwise a bug
+               } // else, do nothing
+       }
+       { // collect pileup information
+               int op, l;
+               op = _cop(cigar[s->k]);
+               l = _cln(cigar[s->k]);
+               p->is_del = p->indel = p->is_refskip = 0;
+               if (op == BAM_CMATCH) {
+                       p->qpos = s->y + (pos - s->x);
+                       if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
+                               int op2 = _cop(cigar[s->k+1]);
+                               int l2 = _cln(cigar[s->k+1]);
+                               if (op2 == BAM_CDEL) p->indel = -(int)l2;
+                               else if (op2 == BAM_CINS) p->indel = l2;
+                               else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
+                                       op2 = _cop(cigar[s->k+2]); l2 = _cln(cigar[s->k+2]);
+                                       if (op2 == BAM_CDEL) p->indel = -(int)l2;
+                                       else if (op2 == BAM_CINS) p->indel = l2;
+                               }
                        }
-                       x += l;
-               } else if (op == BAM_CREF_SKIP) x += l;
-               else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
-               if (is_restart) is_restart ^= (op == BAM_CMATCH);
-               else is_restart ^= (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
-               if (x > pos) {
-                       if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
-                       break;
-               }
+               } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+                       p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
+                       p->is_refskip = (op == BAM_CREF_SKIP);
+               } // cannot be other operations; otherwise a bug
+               p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
        }
-       assert(x > pos); // otherwise a bug
-       return ret;
+       return 1;
 }
 
 /* --- END: Auxiliary functions */
@@ -187,7 +205,7 @@ const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_
                                        iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
                                }
                                iter->plp[n_plp].b = &p->b;
-                               if (resolve_cigar(iter->plp + n_plp, iter->pos)) ++n_plp; // skip the read if we are looking at ref-skip
+                               if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
                        }
                }
                iter->head = iter->dummy->next; // dummy->next may be changed
@@ -221,6 +239,7 @@ int bam_plp_push(bam_plp_t iter, const bam1_t *b)
                if (b->core.flag & iter->flag_mask) return 0;
                bam_copy1(&iter->tail->b, b);
                iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
+               iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
                if (b->core.tid < iter->max_tid) {
                        fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
                        iter->error = 1;

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 4bdc351e18a38322bd39dac30433aea3212b3b5a..cf98f69565ee6d52176df5ca5c9d14a44d2ef3e6 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -91,6 +91,21 @@ static khash_t(64) *load_pos(const char *fn, bam_header_t *h)
        return hash;
 }
 
+static inline int printw(int c, FILE *fp)
+{
+       char buf[16];
+       int l, x;
+       if (c == 0) return fputc('0', fp);
+       for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+       if (c < 0) buf[l++] = '-';
+       buf[l] = 0;
+       for (x = 0; x < l/2; ++x) {
+               int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+       }
+       fputs(buf, fp);
+       return 0;
+}
+
 // an analogy to pileup_func() below
 static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu, void *data)
 {
@@ -162,7 +177,10 @@ static int glt3_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pu,
 
 static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
 {
-       if (p->is_head) printf("^%c", p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+       if (p->is_head) {
+               putchar('^');
+               putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
+       }
        if (!p->is_del) {
                int j, rb, c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
                rb = (ref && pos < ref_len)? ref[pos] : 'N';
@@ -170,19 +188,19 @@ static void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char
                else c = bam1_strand(p->b)? tolower(c) : toupper(c);
                putchar(c);
                if (p->indel > 0) {
-                       printf("+%d", p->indel);
+                       putchar('+'); printw(p->indel, stdout);
                        for (j = 1; j <= p->indel; ++j) {
                                c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
                                putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
                        }
                } else if (p->indel < 0) {
-                       printf("%d", p->indel);
+                       printw(p->indel, stdout);
                        for (j = 1; j <= -p->indel; ++j) {
                                c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
                                putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
                        }
                }
-       } else putchar('*');
+       } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
        if (p->is_tail) putchar('$');
 }
 
@@ -256,12 +274,17 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                }
        }
        // print the first 3 columns
-       printf("%s\t%d\t%c\t", d->h->target_name[tid], pos + 1, rb);
+       fputs(d->h->target_name[tid], stdout); putchar('\t');
+       printw(pos+1, stdout); putchar('\t'); putchar(rb); putchar('\t');
        // print consensus information if required
-       if (d->format & BAM_PLF_CNS)
-               printf("%c\t%d\t%d\t%d\t", bam_nt16_rev_table[cns>>28], cns>>8&0xff, cns&0xff, cns>>16&0xff);
+       if (d->format & BAM_PLF_CNS) {
+               putchar(bam_nt16_rev_table[cns>>28]); putchar('\t');
+               printw(cns>>8&0xff, stdout); putchar('\t');
+               printw(cns&0xff, stdout); putchar('\t');
+               printw(cns>>16&0xff, stdout); putchar('\t');
+       }
        // print pileup sequences
-       printf("%d\t", n);
+       printw(n, stdout); putchar('\t');
        rms_aux = 0; // we need to recalculate rms_mapq when -c is not flagged on the command line
        for (i = 0; i < n; ++i) {
                const bam_pileup1_t *p = pu + i;
@@ -310,7 +333,7 @@ static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *p
                for (i = 0; i < n; ++i) {
                        int x = pu[i].qpos;
                        int l = pu[i].b->core.l_qseq;
-                       printf("%d,", x < l/2? x+1 : -((l-1)-x+1));
+                       printw(x < l/2? x+1 : -((l-1)-x+1), stdout); putchar(',');
                }
        }
        putchar('\n');

diff --git a/bam_tview.c b/bam_tview.c
index 24cd12a5bf743dba2948ee92bd9c5c490c30e4ce..e48afa7bd4add26404fecc04d6548e7b3989927b 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -109,7 +109,7 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
                                                        if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
                                                }
                                        }
-                               } else c = '*';
+                               } else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
                        } else { // padding
                                if (j > p->indel) c = '*';
                                else { // insertion

diff --git a/bamtk.c b/bamtk.c
index 4de99d7482e5c35c7f682ad68a49a0bf3526afdf..fb0e3888476e6e9e51fe28a92bc709af03fbb25d 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-19 (r777)"
+#define PACKAGE_VERSION "0.1.8-20 (r778)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);