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DASrealign.c
1176 lines (1028 loc) · 36.3 KB
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DASrealign.c
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/************************************************************************************\
* *
* Copyright (c) 2015, Dr. Eugene W. Myers (EWM). All rights reserved. *
* *
* Redistribution and use in source and binary forms, with or without modification, *
* are permitted provided that the following conditions are met: *
* *
* · Redistributions of source code must retain the above copyright notice, this *
* list of conditions and the following disclaimer. *
* *
* · Redistributions in binary form must reproduce the above copyright notice, this *
* list of conditions and the following disclaimer in the documentation and/or *
* other materials provided with the distribution. *
* *
* · The name of EWM may not be used to endorse or promote products derived from *
* this software without specific prior written permission. *
* *
* THIS SOFTWARE IS PROVIDED BY EWM ”AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, *
* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND *
* FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL EWM BE LIABLE *
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES *
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS *
* OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN *
* IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
* *
* For any issues regarding this software and its use, contact EWM at: *
* *
* Eugene W. Myers Jr. *
* Bautzner Str. 122e *
* 01099 Dresden *
* GERMANY *
* Email: gene.myers@gmail.com *
* *
\************************************************************************************/
/*******************************************************************************************
*
* Map and extend every overlap to the patched read framework.
*
* Author: Gene Myers
* Date : March 2015
*
*******************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include <unistd.h>
#include <stdint.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "DB.h"
#include "align.h"
#undef OUTLINE
#undef SHOW_MAP
#undef TRACE
#undef SHOW_FINAL
#undef SHOW_ALIGNMENTS
static char *Usage = " [-v] [-l<int(800)>] <block1:db> <block2:db> <source:las> <target:las>";
static int TRACE_SPACING; // Trace spacing (from .las file)
static int TBYTES; // Bytes per trace segment (from .las file)
static int SMALL; // Trace points can fit in a byte
static int MIN_LEN; // Minimum piece length
static DAZZ_DB _ADB, *ADB = &_ADB; // A-read database
static DAZZ_DB _BDB, *BDB = &_BDB; // B-read database
static int ADB_ofirst, ADB_olast;
static int BDB_ofirst, BDB_olast;
static int AFIRST, BFIRST;
static int64 *AMAP_IDX; // Map to originals for A-reads
static int *AMAP;
static int64 *BMAP_IDX; // Map to orignals for B-reads
static int *BMAP;
static int *IAMAP, *IBMAP; // Inverse map, old x -> new IMAP[x]..IMAP[x+1]-1
static FILE *OUTPUT; // The new set of overlaps
static int64 WOVLS;
static int VERBOSE;
int lowTK(int a)
{ return (a/TRACE_SPACING); }
int hghTK(int a)
{ return ((a+(TRACE_SPACING-1))/TRACE_SPACING); }
int lowTP(int a)
{ return ((a/TRACE_SPACING)*TRACE_SPACING); }
/*******************************************************************************************
*
* Finger iterator: allows one to map the next trace point of a read to its
* patched read as the trace points are examined in order.
*
*******************************************************************************************/
typedef struct
{ int cidx;
int lidx;
int dist;
int last;
int blen;
int *map;
} Finger;
// A finger is initialized with init_finger where cur is suppled by the user, and the
// patch sequence is in GRIM[gb..ge].
static inline void init_finger(Finger *f, int *map, int mb, int me, int blen)
{ if (blen == 0)
{ f->cidx = mb+3;
f->lidx = me;
f->last = map[mb];
}
else
{ f->cidx = me-4;
f->lidx = mb-1;
f->last = blen - map[me-1];
}
f->dist = 0;
f->blen = blen;
f->map = map;
}
// Advance finger to position pos and return position in patched read, if known, -1 otherwise
static inline int good(Finger *cur, int pos)
{ int blen, *map;
map = cur->map;
blen = cur->blen;
if (blen == 0)
{ while (cur->cidx < cur->lidx && pos >= map[cur->cidx])
{ cur->dist += (map[cur->cidx-2] - cur->last) + map[cur->cidx-1];
cur->last = map[cur->cidx];
cur->cidx += 3;
}
if (pos <= map[cur->cidx-2])
{ if (pos < cur->last)
return (-1);
else
return (cur->dist + (pos-cur->last));
}
}
else
{ while (cur->cidx > cur->lidx && pos >= blen - map[cur->cidx])
{ cur->dist += ((blen - map[cur->cidx+2]) - cur->last) + map[cur->cidx+1];
cur->last = blen - map[cur->cidx];
cur->cidx -= 3;
}
if (pos <= blen - map[cur->cidx+2])
{ if (pos < cur->last)
return (-1);
else
return (cur->dist + (pos-cur->last));
}
}
return (-1);
}
// Advance finger to position pos, and return best estimate of position in patched read,
// or -1 if outside the bounds of the patched read. acc points at the distance the
// estimate is from a non-patched segment (0 if mapped).
static inline int where(Finger *cur, int pos, int *acc)
{ int blen, *map;
map = cur->map;
blen = cur->blen;
if (blen == 0)
{ while (cur->cidx < cur->lidx && pos >= map[cur->cidx])
{ cur->dist += (map[cur->cidx-2] - cur->last) + map[cur->cidx-1];
cur->last = map[cur->cidx];
cur->cidx += 3;
}
if (pos <= map[cur->cidx-2])
{ if (pos < cur->last)
return (-1);
else
{ *acc = 0;
return (cur->dist + (pos-cur->last));
}
}
if (cur->cidx >= cur->lidx)
return (-1);
else
{ int ab, ae;
ab = map[cur->cidx-2];
ae = map[cur->cidx];
if (pos-ab < ae-pos)
*acc = pos-ab;
else
*acc = ae-pos;
return (cur->dist + (ab-cur->last) + ((1.*(pos-ab))/(ae-ab)) * map[cur->cidx-1]);
}
}
else
{ while (cur->cidx > cur->lidx && pos >= blen - map[cur->cidx])
{ cur->dist += ((blen - map[cur->cidx+2]) - cur->last) + map[cur->cidx+1];
cur->last = blen - map[cur->cidx];
cur->cidx -= 3;
}
if (pos <= blen - map[cur->cidx+2])
{ if (pos < cur->last)
return (-1);
else
{ *acc = 0;
return (cur->dist + (pos-cur->last));
}
}
if (cur->cidx <= cur->lidx)
return (-1);
else
{ int ab, ae;
ab = blen - map[cur->cidx+2];
ae = blen - map[cur->cidx];
if (pos-ab < ae-pos)
*acc = pos-ab;
else
*acc = ae-pos;
return (cur->dist + (ab-cur->last) + ((1.*(pos-ab))/(ae-ab)) * map[cur->cidx+1]);
}
}
}
/*******************************************************************************************
*
* Trace point mapping:
* recon makes a trace with all the mapable pairs
* when there are no mapable pairs, estimate finds the estimated point position closest
* to a mapable region.
*
*******************************************************************************************/
static int recon(Path *image, Path *path, Finger *afinger, Finger *bfinger)
{ static int tmax = -1;
static uint16 *itrace = NULL;
int ae, be;
int al, bl;
int an, bn;
int t, tl, df;
uint16 *strace = ((uint16 *) (path->trace));
if (path->tlen > tmax)
{ tmax = 1.2*path->tlen + 100;
itrace = (uint16 *) Realloc(itrace,sizeof(uint16)*tmax,"Reallocating image trace");
}
image->trace = itrace;
#ifdef TRACE
printf(" Backbone:\n");
fflush(stdout);
#endif
df = 0;
tl = -1;
al = bl = 0;
ae = lowTP(path->abpos);
be = path->bbpos;
if ((an = good(afinger,path->abpos)) >= 0 && (bn = good(bfinger,be)) >= 0)
{ image->abpos = al = an;
image->bbpos = bl = bn;
tl = 0;
#ifdef TRACE
printf(" %5d,%5d -> %5d,%5d\n",path->abpos,be,an,bn);
fflush(stdout);
#endif
}
for (t = 1; t < path->tlen; t += 2)
{ ae += TRACE_SPACING;
be += strace[t];
if (ae > path->aepos)
ae = path->aepos;
if (tl >= 0)
df += strace[t-1];
if ((an = good(afinger,ae)) >= 0 && (bn = good(bfinger,be)) >= 0)
{ if (tl < 0)
{ image->abpos = an;
image->bbpos = bn;
tl = 0;
}
else
{ itrace[tl] = an-al;
itrace[tl+1] = bn-bl;
tl += 2;
}
image->aepos = al = an;
image->bepos = bl = bn;
image->diffs = df;
#ifdef TRACE
printf(" %5d,%5d -> %5d,%5d\n",ae,be,an,bn);
fflush(stdout);
#endif
}
}
image->tlen = tl;
if (tl <= 0)
return (0);
else
return (1);
}
static int estimate(Path *path, Finger *afinger, Finger *bfinger, int *bsta, int *bstb, int *acc)
{ int ae, be;
int an, bn;
int best, adst, bdst;
int t;
uint16 *strace = ((uint16 *) (path->trace));
*bsta = *bstb = -1;
best = INT32_MAX;
#ifdef TRACE
printf(" Point Estimate:\n");
fflush(stdout);
#endif
ae = lowTP(path->abpos);
be = path->bbpos;
if ((an = where(afinger,path->abpos,&adst)) >= 0 && (bn = where(bfinger,be,&bdst)) >= 0)
{ best = adst + bdst;
*bsta = an;
*bstb = bn;
#ifdef TRACE
printf(" %5d,%5d -> %5d(%d),%5d(%d)\n",path->abpos,be,an,adst,bn,bdst);
fflush(stdout);
#endif
}
for (t = 1; t < path->tlen; t += 2)
{ ae += TRACE_SPACING;
be += strace[t];
if (ae > path->aepos)
ae = path->aepos;
if ((an = where(afinger,ae,&adst)) >= 0 && (bn = where(bfinger,be,&bdst)) >= 0)
{ if (adst + bdst < best)
{ best = adst + bdst;
*bsta = an;
*bstb = bn;
}
#ifdef TRACE
printf(" %5d,%5d -> %5d(%d),%5d(%d)\n",ae,be,an,adst,bn,bdst);
fflush(stdout);
#endif
}
}
*acc = best;
return (*bsta >= 0);
}
#ifdef SHOW_MAP
static void print_map(int *map, int mb, int me, int clen)
{ int b, dist;
if (clen == 0)
{ printf(" n");
for (b = mb; b < me; b += 3)
{ printf(" [%5d,%5d]",map[b],map[b+1]);
if (b+2 < me)
printf(" %5d",map[b+2]);
}
printf("\n");
printf(" ");
dist = 0;
for (b = mb; b < me; b += 3)
{ printf(" [%5d,%5d]",dist,dist+(map[b+1]-map[b]));
dist += map[b+1]-map[b];
if (b+2 < me)
{ printf(" %5d",map[b+2]);
dist += map[b+2];
}
}
printf("\n");
}
else
{ printf(" c");
for (b = me; b >= mb; b -= 3)
{ printf(" [%5d,%5d]",clen-map[b-1],clen-map[b-2]);
if (b-3 > mb)
printf(" %5d",map[b-3]);
}
printf("\n");
printf(" ");
dist = 0;
for (b = me; b >= mb; b -= 3)
{ printf(" [%5d,%5d]",dist,dist+(map[b-1]-map[b-2]));
dist += map[b-1]-map[b-2];
if (b-3 > mb)
{ printf(" %5d",map[b-3]);
dist += map[b-3];
}
}
printf("\n");
}
}
#endif
#ifdef SHOW_FINAL
static void show_overlap(Overlap *ovl)
{ int i, a, b;
uint16 *t;
t = (uint16 *) (ovl->path.trace);
a = ovl->path.abpos;
b = ovl->path.bbpos;
for (i = 0; i < ovl->path.tlen; i += 2)
{ a += t[i];
b += t[i+1];
printf(" %5d %5d :: %5d %5d\n",t[i],t[i+1],a,b);
fflush(stdout);
}
}
#endif
static void convert_trace(Path *path)
{ int ab, ae;
int t;
uint16 *trace = ((uint16 *) (path->trace));
ae = lowTP(path->abpos);
ab = path->abpos;
for (t = 0; t < path->tlen; t += 2)
{ ae += TRACE_SPACING;
if (ae > path->aepos)
ae = path->aepos;
#ifdef TRACE
printf(" %5d,%5d -> %5d,%5d\n",trace[t],trace[t+1],ae-ab,trace[t+1]);
fflush(stdout);
#endif
trace[t] = ae-ab;
ab = ae;
}
}
// Produce the concatentation of path1 and path2 where they are known to meet at
// the trace point with coordinate ap. Place this result in a big growing buffer,
// that gets reset when fusion is called with path1 = NULL
static void fusion(Path *path1, Path *path2, int wch)
{ static uint16 *paths = NULL;
static int pmax = 0;
static int ptop = 0;
int k;
int len;
uint16 *trace;
if (path1 == NULL)
{ ptop = 0;
return;
}
len = path1->tlen + path2->tlen;
if (ptop + len >= pmax)
{ pmax = 1.2*(ptop+len) + 1000;
paths = (uint16 *) Realloc(paths,sizeof(uint16)*pmax,"Allocating paths");
if (paths == NULL)
exit (1);
}
trace = paths+ptop;
ptop += len;
len = 0;
if (path1->tlen > 0)
{ uint16 *t = (uint16 *) (path1->trace);
for (k = 0; k < path1->tlen; k += 2)
{ trace[len++] = t[k];
trace[len++] = t[k+1];
}
}
if (path2->tlen > 0)
{ uint16 *t = (uint16 *) (path2->trace);
for (k = 0; k < path2->tlen; k += 2)
{ trace[len++] = t[k];
trace[len++] = t[k+1];
}
}
if (wch == 1)
{ path1->aepos = path2->aepos;
path1->bepos = path2->bepos;
path1->diffs += path2->diffs;
path1->trace = trace;
path1->tlen = len;
}
else
{ path2->abpos = path1->abpos;
path2->bbpos = path1->bbpos;
path2->diffs += path1->diffs;
path2->trace = trace;
path2->tlen = len;
}
}
static void EXTENDER(int aread, Overlap *ovls, int novl)
{ Finger _afinger, *afinger = &_afinger;
Finger _bfinger, *bfinger = &_bfinger;
static Overlap _ovla, *ovla = &_ovla;
static Path *ipath = &_ovla.path;
static Path rpath, fpath;
static Alignment _ralign, *ralign = &_ralign;
static Alignment _falign, *falign = &_falign;
static Work_Data *work = NULL;
static Align_Spec *spec;
int ap, alast;
if (aread < ADB_ofirst || aread >= ADB_olast)
return;
if (work == NULL)
{ spec = New_Align_Spec(.70,100,ADB->freq,1);
work = New_Work_Data();
ralign->path = &rpath;
falign->path = &fpath;
}
alast = IAMAP[aread+1];
for (ap = IAMAP[aread]; ap < alast; ap++)
{ int mb, me;
int aend, abeg, alen;
mb = AMAP_IDX[ap]+2;
me = AMAP_IDX[ap+1];
abeg = AMAP[mb];
aend = AMAP[me-1];
if (aend - abeg < MIN_LEN)
continue;
ralign->aseq = falign->aseq = ((char *) ADB->bases) + ADB->reads[ap].boff;
ralign->alen = falign->alen = alen = ADB->reads[ap].rlen;
#ifdef OUTLINE
printf("AREAD %d -> %d [%d,%d]\n",aread,ap,abeg,aend);
fflush(stdout);
#endif
#ifdef SHOW_MAP
print_map(AMAP,mb,me,0);
#endif
{ int o, ob, oe;
Path *path;
int bread;
int bp, blast;
for (ob = 0; ob < novl; ob = oe)
{ bread = ovls[ob].bread;
for (oe = ob+1; oe < novl && ovls[oe].bread == bread; oe += 1)
;
if (bread < BDB_ofirst || bread >= BDB_olast)
continue;
blast = IBMAP[bread+1];
for (bp = IBMAP[bread]; bp < blast; bp++)
{ int hb, he;
int bend, bbeg, blen;
int alpos, clen;
hb = BMAP_IDX[bp]+2;
he = BMAP_IDX[bp+1];
bbeg = BMAP[hb];
bend = BMAP[he-1];
if (bend - bbeg < MIN_LEN)
continue;
#ifdef OUTLINE
printf(" BREAD %d->%d [%d,%d]\n",bread,bp,bbeg,bend);
fflush(stdout);
#endif
#ifdef SHOW_MAP
print_map(BMAP,hb,he,0);
#endif
alpos = -1;
for (o = ob; o < oe; o++)
{ int bbreal, bereal;
path = &(ovls[o].path);
if (COMP(ovls[o].flags))
{ clen = BMAP[hb-1];
bbreal = clen-path->bepos;
bereal = clen-path->bbpos;
}
else
{ clen = 0;
bbreal = path->bbpos;
bereal = path->bepos;
}
#ifdef OUTLINE
printf(" OVL %d: [%d,%d] %c [%d,%d]\n",o,
path->abpos,path->aepos,(clen==0)?'n':'c',bbreal,bereal);
fflush(stdout);
#endif
if (path->abpos <= aend-MIN_LEN && path->aepos >= abeg+MIN_LEN &&
bbreal <= bend-MIN_LEN && bereal >= bbeg+MIN_LEN)
{ ralign->bseq = falign->bseq = ((char *) BDB->bases) + BDB->reads[bp].boff;
ralign->blen = falign->blen = blen = BDB->reads[bp].rlen;
ralign->flags = falign->flags = ovls[o].flags;
if (COMP(ralign->flags))
Complement_Seq(ralign->bseq,blen);
#ifdef SHOW_MAP
print_map(BMAP,hb,he,clen);
#endif
init_finger(afinger,AMAP,mb,me,0);
init_finger(bfinger,BMAP,hb,he,clen);
if ( ! recon(ipath,path,afinger,bfinger))
{ int apos, bpos, acc, len, diag;
init_finger(afinger,AMAP,mb,me,0);
init_finger(bfinger,BMAP,hb,he,clen);
if (estimate(path,afinger,bfinger,&apos,&bpos,&acc))
if (apos > alpos)
{ diag = apos-bpos;
acc /= 2;
if (apos + acc > alen)
acc = alen-apos;
if (bpos + acc > blen)
acc = blen-bpos;
if (apos < acc)
acc = apos;
if (bpos < acc)
acc = bpos;
if (acc > 500)
acc = 500;
acc *= 2;
#ifdef OUTLINE
printf(" Trying: %d,%d + %d\n",apos,bpos,acc);
fflush(stdout);
#endif
Local_Alignment(ralign,work,spec,
diag-acc,diag+acc,apos+bpos,-1,-1);
#ifdef OUTLINE
printf(" Local: <%d,%d> -> <%d,%d>\n",
ralign->path->abpos,ralign->path->bbpos,
ralign->path->aepos,ralign->path->bepos);
fflush(stdout);
#endif
len = ralign->path->aepos - ralign->path->abpos;
if (len >= MIN_LEN && ralign->path->diffs <= .35*len)
{ ovla->aread = ap;
ovla->bread = bp;
ovla->flags = ralign->flags;
_ovla.path = *(ralign->path);
convert_trace(ralign->path);
#ifdef OUTLINE
printf(" Final: %d[%d..%d] vs %d[%d..%d] %c d=%d\n",
ovla->aread,ovla->path.abpos,ovla->path.aepos,
ovla->bread,ovla->path.bbpos,ovla->path.bepos,
(COMP(ovla->flags) ? 'c' : 'n'), ovla->path.diffs);
fflush(stdout);
#endif
#ifdef SHOW_FINAL
show_overlap(ovla);
#endif
#ifdef SHOW_ALIGNMENTS
Compute_Trace_IRR(ralign,work,GREEDIEST);
Print_Alignment(stdout,ralign,work,4,80,10,0,6);
#else
Write_Overlap(OUTPUT,ovla,sizeof(uint16));
WOVLS += 1;
#endif
alpos = ralign->path->aepos;
#ifdef OUTLINE
printf(" ACCEPT\n");
#endif
}
#ifdef OUTLINE
else
printf(" REJECT\n");
#endif
}
#ifdef OUTLINE
else
printf(" SKIP\n");
else
printf(" NO OVERLAP\n");
fflush(stdout);
#endif
}
else if (ipath->aepos > alpos)
{ int ab, bb;
int ae, be;
int ar, br;
int af, bf;
ab = ipath->abpos;
bb = ipath->bbpos;
ae = ipath->aepos;
be = ipath->bepos;
ar = ab;
br = bb;
if (ab > 0 && bb > 0)
{ Find_Extension(ralign,work,spec,ab-bb,ab+bb,-1,-1,1);
ar = ralign->path->abpos;
br = ralign->path->bbpos;
#ifdef OUTLINE
printf(" Rev: (%d,%d)",ab,bb);
printf(" -> (%d,%d)",ar,br);
printf(" %d",ralign->path->diffs);
fflush(stdout);
#endif
if (ar == 0 || br == 0 || ralign->path->diffs <= .35*(ab-ar))
{
#ifdef OUTLINE
printf(" OK\n");
fflush(stdout);
#endif
if (ab - 10 < ar)
{ uint16 *trace = (uint16 *) ipath->trace;
int tlen = ipath->tlen;
if (tlen > 0)
{ trace[0] += ab - ar;
trace[1] += bb - br;
}
ipath->abpos = ar;
ipath->bbpos = br;
}
else
{ convert_trace(ralign->path);
fusion(ralign->path,ipath,2);
}
}
else
{ ar = ab;
br = bb;
#ifdef OUTLINE
printf(" NOTOK\n");
fflush(stdout);
#endif
}
}
af = ae;
bf = be;
if (ae < alen && be < blen)
{ Find_Extension(falign,work,spec,ae-be,ae+be,-1,-1,0);
af = falign->path->aepos;
bf = falign->path->bepos;
#ifdef OUTLINE
printf(" Fow: (%d,%d)",ae,be);
printf(" -> (%d,%d)",af,bf);
printf(" %d",falign->path->diffs);
fflush(stdout);
#endif
if (af == alen || bf == blen || falign->path->diffs <= .35*(af-ae))
{
#ifdef OUTLINE
printf(" OK\n");
fflush(stdout);
#endif
if (ae + 10 > af)
{ uint16 *trace = (uint16 *) ipath->trace;
int tlen = ipath->tlen;
if (tlen > 0)
{ trace[tlen-2] += af-ae;
trace[tlen-1] += bf-be;
}
ipath->aepos = af;
ipath->bepos = bf;
}
else
{ convert_trace(falign->path);
fusion(ipath,falign->path,1);
}
}
else
{ af = ae;
bf = be;
#ifdef OUTLINE
printf(" NOTOK\n");
fflush(stdout);
#endif
}
}
alpos = af;
if (af-ar >= MIN_LEN)
{ ovla->aread = AFIRST + ap;
ovla->bread = BFIRST + bp;
ovla->flags = ralign->flags;
#ifdef OUTLINE
printf(" Final: %d[%d..%d] vs %d[%d..%d] %c d=%d\n",
ovla->aread,ovla->path.abpos,ovla->path.aepos,
ovla->bread,ovla->path.bbpos,ovla->path.bepos,
(COMP(ovla->flags) ? 'c' : 'n'), ovla->path.diffs);
fflush(stdout);
#endif
#ifdef SHOW_FINAL
show_overlap(ovla);
#endif
#ifdef SHOW_ALIGNMENTS
fpath = *ipath;
Compute_Trace_IRR(falign,work,GREEDIEST);
Print_Alignment(stdout,falign,work,4,80,10,0,6);
#else
Write_Overlap(OUTPUT,ovla,sizeof(uint16));
WOVLS += 1;
#endif
}
#ifdef OUTLINE
else
printf(" NO OVERLAP\n");
#endif
fusion(NULL,NULL,0);
}
#ifdef OUTLINE
else
printf(" SKIP\n");
fflush(stdout);
#endif
if (COMP(ralign->flags))
Complement_Seq(ralign->bseq,blen);
}
}
}
}
}
}
}
static int make_a_pass(FILE *input, void (*ACTION)(int, Overlap *, int), int trace)
{ static Overlap *ovls = NULL;
static int omax = 500;
static uint16 *paths = NULL;
static int pmax = 100000;
int64 i, j, novl;
int n, a;
int pcur;
int max;
if (ovls == NULL)
{ ovls = (Overlap *) Malloc(sizeof(Overlap)*omax,"Allocating overlap buffer");
if (ovls == NULL)
exit (1);
}
if (trace && paths == NULL)
{ paths = (uint16 *) Malloc(sizeof(uint16)*pmax,"Allocating path buffer");
if (paths == NULL)
exit (1);
}
rewind(input);
fread(&novl,sizeof(int64),1,input);
fread(&TRACE_SPACING,sizeof(int),1,input);
if (TRACE_SPACING <= TRACE_XOVR)
{ TBYTES = sizeof(uint8);
SMALL = 1;
}
else
{ TBYTES = sizeof(uint16);
SMALL = 0;
}
if (Read_Overlap(input,ovls) != 0)
ovls[0].aread = INT32_MAX;
else if (trace)
{ if (ovls[0].path.tlen > pmax)
{ pmax = 1.2*(ovls[0].path.tlen)+10000;
paths = (uint16 *) Realloc(paths,sizeof(uint16)*pmax,"Expanding path buffer");
if (paths == NULL) exit (1);
}
fread(paths,TBYTES,ovls[0].path.tlen,input);
if (TBYTES == 1)
{ ovls[0].path.trace = paths;
Decompress_TraceTo16(ovls);
}
}
else
fseek(input,TBYTES*ovls[0].path.tlen,SEEK_CUR);
pcur = 0;
n = max = 0;
for (j = ovls[0].aread; j < ADB_olast; j++)
{ ovls[0] = ovls[n];
a = ovls[0].aread;
if (a != j)
n = 0;
else
{ if (trace)
memmove(paths,paths+pcur,sizeof(uint16)*ovls[0].path.tlen);
n = 1;
pcur = ovls[0].path.tlen;
while (1)
{ if (Read_Overlap(input,ovls+n) != 0)
{ ovls[n].aread = INT32_MAX;
break;
}
if (trace)
{ if (pcur + ovls[n].path.tlen > pmax)
{ pmax = 1.2*(pcur+ovls[n].path.tlen)+10000;
paths = (uint16 *) Realloc(paths,sizeof(uint16)*pmax,"Expanding path buffer");
if (paths == NULL) exit (1);
}
fread(paths+pcur,TBYTES,ovls[n].path.tlen,input);
if (TBYTES == 1)
{ ovls[n].path.trace = paths+pcur;
Decompress_TraceTo16(ovls+n);
}
}
else
fseek(input,TBYTES*ovls[n].path.tlen,SEEK_CUR);
if (ovls[n].aread != a)
break;
pcur += ovls[n].path.tlen;
n += 1;
if (n >= omax)
{ omax = 1.2*n + 100;
ovls = (Overlap *) Realloc(ovls,sizeof(Overlap)*omax,"Expanding overlap buffer");
if (ovls == NULL) exit (1);
}
}
if (n >= max)
max = n;
pcur = 0;
for (i = 0; i < n; i++)
{ ovls[i].path.trace = paths+pcur;
pcur += ovls[i].path.tlen;
}
}
if (j >= ADB_ofirst)
ACTION(j,ovls,n);
}
if (ovls[n].aread < INT32_MAX)
{ fprintf(stderr,"%s: .las file overlaps don't correspond to reads in block %d of DB\n",
Prog_Name,ADB->part);
exit (1);
}
return (max);
}
int main(int argc, char *argv[])
{ DAZZ_TRACK *map1, *map2;
// Process arguments
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("DASrealign")
MIN_LEN = 800;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("v")