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MerquryFK.c
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MerquryFK.c
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/********************************************************************************************
*
* Refactoring of Merqury CN-spectra script as a command line tool using FastK
*
* Author: Gene Myers
* Date : March, 2021
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <dirent.h>
#include <math.h>
#define DEBUG
#include "libfastk.h"
#include "cn_plotter.h"
#include "asm_plotter.h"
#include "hap_plotter.h"
#include "blk_plot.R.h"
// Phase Block parameters
static int ANCHOR_MARK = 5;
static int ANCHOR_LENGTH = 20000;
// Usage
static char *Usage[5] = { " [-w<double(6.0)>] [-h<double(4.5)>]",
" [-[xX]<number(x2.1)>] [-[yY]<number(y1.1)>]",
" [-vk] [-lfs] [-pdf] [-z] [-T<int(4)>] [-P<dir(/tmp)>]",
" <read>[.ktab] [ <mat>[.hap[.ktab]] <pat>[.hap[.ktab]] ]",
" <asm1:dna> [<asm2:dna>] <out>"
};
// Expected inputs from FastK ...
// READS.hist FastK -t1 -kKMER [...] <read_data> -NREADS
// READS.ktab
// MAT.hap.ktab HAPmaker MAT PAT READS
// PAT.hap.ktab
//
// Outputs:
// OUT.ASM[i].spectra-cn.*
// OUT.spectra-asm.*
// OUT.spectra-cn.* (if 2 haploids)
// OUT.qv
// OUT.ASM[i].qv
// OUT.ASM[i]_only.bed
// OUT.completeness.stats
// TRIO Outputs:
// OUT.ASM[i].HAP.spectra-cn.*
// OUT.hapmers.blob.*
// OUT.ASM[i].phased_block.bed
// OUT.ASM[i].phased_block.stats
// OUT.ASM[i].phased_block.blob.*
// OUT.ASM[i].block.N.[pdf|png]
// OUT.ASM[i].continuity.N.[pdf|png]
static char template[20] = "._MQY_GEN.XXXXXX";
static char templateA1[20] = "._MQY_A1.XXXXXX";
static char templateA2[20] = "._MQY_A2.XXXXXX";
static char *templateA[2] = { templateA1, templateA2 };
static char templateR1[20] = "._MQY_R1.XXXXXX";
static char templateR2[20] = "._MQY_R2.XXXXXX";
static char *templateR[2] = { templateR1, templateR2 };
static char templateM1[20] = "._MQY_M1.XXXXXX";
static char templateM2[20] = "._MQY_M2.XXXXXX";
static char *templateM[2] = { templateM1, templateM2 };
static char templateP1[20] = "._MQY_P1.XXXXXX";
static char templateP2[20] = "._MQY_P2.XXXXXX";
static char *templateP[2] = { templateP1, templateP2 };
static int VERBOSE;
static int KMER;
static int SOLID_THRESH;
static int64 SOLID_COUNT;
// In a scan of an assembly's profile and relative read profile:
// Compute per-scaffold qv in <out>.<asmb>.qv, and output a bed
// file of 0-read count intervals in <out>.<asmb>_only.bed
// Return the total # of bp's and the total # of 0-read counts.
static int64 *scan_asm(char *atab, char *aprf, char *aroot, char *rroot, char *out)
{ static int64 summary[2];
Profile_Index *AP, *RP;
FILE *qvs, *bed;
uint16 *aprof, *rprof;
int64 pmax, plen;
int i, x, last;
int64 miss, tots;
int64 TOTS, MISS;
double err, qv;
if (VERBOSE)
fprintf(stderr,"\n Making .qv and .bed files for assembly %s\n",aroot);
AP = Open_Profiles(atab);
RP = Open_Profiles(aprf);
if (AP == NULL)
{ fprintf(stderr,"\n%s: Cannot open/find FastK profile for assembly %s\n",Prog_Name,aroot);
exit (1);
}
if (RP == NULL)
{ fprintf(stderr,"\n%s: Cannot open/find FastK relative profile of %s against assembly %s\n",
Prog_Name,rroot,aroot);
exit (1);
}
if (AP->kmer != KMER)
{ fprintf(stderr,"\n%s: Profile of assembly %s has wrong k-mer size %d != %d\n",
Prog_Name,aroot,AP->kmer,KMER);
exit (1);
}
if (RP->kmer != KMER)
{ fprintf(stderr,"\n%s: Relative profile of %s against assembly %s has wrong k-mer size",
Prog_Name,rroot,aroot);
fprintf(stderr," %d != %d\n",RP->kmer,KMER);
exit (1);
}
pmax = 20000;
aprof = Malloc(2*pmax*sizeof(uint16),"Profile array");
rprof = aprof + pmax;
bed = fopen(Catenate(out,".",aroot,"_only.bed"),"w");
qvs = fopen(Catenate(out,".",aroot,".qv"),"w");
fprintf(qvs,"Assembly Only\tTotal\tError %%\tQV\n");
TOTS = 0;
MISS = 0;
for (i = 0; i < AP->nreads; i++)
{ plen = Fetch_Profile(AP,i,pmax,aprof);
if (plen > pmax)
{ pmax = 1.2*plen + 1000;
aprof = Realloc(aprof,2*pmax*sizeof(uint16),"Profile array");
if (aprof == NULL)
exit (1);
rprof = aprof + pmax;
Fetch_Profile(AP,i,pmax,aprof);
}
Fetch_Profile(RP,i,pmax,rprof);
last = -1;
miss = tots = 0;
for (x = 0; x < plen; x++)
{ if (aprof[x] != 0)
{ if (rprof[x] == 0)
{ miss += 1;
if (x > last)
{ if (last > 0)
fprintf(bed,"\t%d\n",last);
fprintf(bed,"%d\t%d",i,x);
}
last = x+KMER;
}
tots += 1;
}
}
if (last > 0)
fprintf(bed,"\t%d\n",last);
err = 1. - pow(1.-(1.*miss)/tots,1./KMER);
qv = -10.*log10(err);
fprintf(qvs,"%lld\t%lld\t%.4f\t%.1f\n",miss,tots,err,qv);
TOTS += tots;
MISS += miss;
}
fclose(bed);
fclose(qvs);
Free_Profiles(RP);
Free_Profiles(AP);
summary[0] = MISS;
summary[1] = TOTS;
return (summary);
}
// Phase block codes: mark record
typedef struct
{ int beg; // interval [beg,end]
int end;
int mrk; // sum of majority marks (+ = hap 1, - = hap 2)
int opp; // sum of minority marks (- = hap 1, + = hap 2)
} Mark;
// mark[0..mtop) is an array of *pure* (opp=0) blocks, partition and merge blocks
// so that no block is unreliable save for the 1st and last, doing so in a way
// that minimized the impurity of the blocks.
static int merge_blocks(int mtop, Mark *mark)
{ int i, j, k;
int last, first;
// First merge adjacent reliable blocks of the same polarity.
last = -1;
j = 0;
for (i = 0; i < mtop; i++, j++)
{ mark[j] = mark[i];
if (mark[i].end-mark[i].beg >= ANCHOR_LENGTH || abs(mark[i].mrk) >= ANCHOR_MARK)
{ if (last >= 0 && (mark[i].mrk < 0) == (mark[last].mrk < 0))
{ for (k = last+1; k < j; k += 2)
{ mark[last].opp += mark[k].mrk;
mark[last].mrk += mark[k+1].mrk;
}
mark[last].end = mark[j].end;
j = last;
}
else
{ if (last < 0)
first = j;
last = j;
}
}
}
mtop = j;
// Now decide how to divide any unreliable blocks between opposite polarity reliable
// blocks to arrive at a final partitioning
if ((mtop-last) % 2 == 0)
{ mark[mtop].beg = mark[mtop].end = mark[mtop-1].end;
mark[mtop].mrk = mark[mtop].opp = 0;
mtop += 1;
}
mark[mtop].mrk = mark[mtop].opp = 0;
mark[mtop].end = mark[mtop-1].end;
mark[mtop].beg = mark[mtop].end - ANCHOR_LENGTH;
if (first % 2 != 0)
{ mark[-1].beg = mark[-1].end = mark[0].beg;
mark[-1].mrk = mark[-1].opp = 0;
last = -2;
}
else
last = -1;
j = 0;
for (i = 0; i <= mtop; i++, j++)
{ mark[j] = mark[i];
if (mark[i].end-mark[i].beg >= ANCHOR_LENGTH || abs(mark[i].mrk) >= ANCHOR_MARK)
{ int score, best, bidx;
score = 0;
for (k = j-1; k > last; k -= 2)
score += mark[k].mrk;
best = abs(score);
bidx = k;
for (k += 2 ; k < j; k += 2)
{ score -= (mark[k-1].mrk + mark[k].mrk);
if (abs(score) < best)
{ best = abs(score);
bidx = k;
}
else if (abs(score) == best && last >= 0 && abs(mark[last].mrk) > abs(mark[j].mrk))
{ best = abs(score);
bidx = k;
}
}
if (last >= 0)
{ for (k = last+2; k <= bidx; k += 2)
{ mark[last].mrk += mark[k].mrk;
mark[last].opp += mark[k-1].mrk;
}
mark[last++].end = mark[bidx].end;
}
else if (bidx >= 0)
{ int tmrk, topp;
tmrk = topp = 0;
for (k = last+2; k <= bidx; k += 2)
{ tmrk += mark[k].mrk;
topp += mark[k-1].mrk;
}
mark[0].mrk = tmrk;
mark[0].opp = topp;
mark[0].end = mark[bidx].end;
last = 1;
}
else
last = 0;
for (k = bidx+2; k < j; k += 2)
{ mark[j].mrk += mark[k-1].mrk;
mark[j].opp += mark[k].mrk;
}
mark[j].beg = mark[bidx+1].beg;
mark[last] = mark[j];
j = last;
}
}
if (mark[j-1].mrk == 0)
j -= 1;
return (j);
}
static int64 BTOT; // block length sum, #, min & max
static int NBLK; // set by phase_blocks, consumed by block_stats
static int BMIN;
static int BMAX;
// In a scan of an assembly's profile and relative hapmer profiles:
// Compute a phased-block partitioning of the contigs of the assembly
// and output them to <out>.<asmb>.phased_block.bed.
// Output temporary files containing the sizes of blocks, contigs,
// and scaffolds in <troot>.[blk+ctg+scf].un (these are later sorted
// and used to produce N-curves.
// Output a listing of each block with its hapmer composition for the
// production of a blob plot of the blocks.
static int phase_blocks(char *aroot, char *mroot, char *proot,
char *aprf, char *mprf, char *pprf,
char *out, char *troot)
{ Profile_Index *AP, *MP, *PP;
FILE *bed, *plot, *fscf, *fctg, *fblk;
uint16 *aprof, *mprof, *pprof;
int64 pmax, plen;
Mark *mark;
int nctg, nscf;
int64 stot, mtot;
int p, i, x;
AP = Open_Profiles(aprf);
MP = Open_Profiles(mprf);
PP = Open_Profiles(pprf);
if (AP == NULL)
{ fprintf(stderr,"\n%s: Cannot open/find FastK self-profile of %s\n",Prog_Name,aroot);
exit (1);
}
if (MP == NULL)
{ fprintf(stderr,"\n%s: Cannot open/find FastK profile of %s relative to %s\n",
Prog_Name,aroot,mroot);
exit (1);
}
if (PP == NULL)
{ fprintf(stderr,"\n%s: Cannot open/find FastK profile of %s relative to %s\n",
Prog_Name,aroot,proot);
exit (1);
}
pmax = 20000;
aprof = Malloc((3*pmax+2)*sizeof(uint16) + (pmax/KMER+4)*sizeof(Mark),"Profile array");
if (aprof == NULL)
exit (1);
mprof = aprof + (pmax+2);
pprof = mprof + pmax;
mark = ((Mark *) (pprof + pmax)) + 1;
fscf = fopen(Catenate(troot,".scf.un","",""),"w");
fctg = fopen(Catenate(troot,".ctg.un","",""),"w");
fblk = fopen(Catenate(troot,".blk.un","",""),"w");
bed = fopen(Catenate(out,".",aroot,".phased_block.bed"),"w");
fprintf(bed,"Scaffold\tStart\tEnd\tPhase\tPurity\tSwitches\tMarkers\n");
plot = fopen(Catenate(out,".",aroot,".phased_block.blob.hpi"),"w");
fprintf(plot,"Block\tRange\t%s\t%s\tSize\n",mroot,proot);
stot = 0;
mtot = 0;
BTOT = 0;
NBLK = 0;
BMIN = 0x7fffffff;
BMAX = 0;
nctg = 0;
nscf = AP->nreads;
for (p = 0; p < nscf; p++)
{ int beg, end, frst;
int mrk, sum;
int eoc, mtop;
plen = Fetch_Profile(AP,p,pmax,aprof);
if (plen > pmax)
{ pmax = 1.2*plen + 1000;
aprof = Realloc(aprof,(3*pmax+2)*sizeof(uint16) + (pmax/KMER+4)*sizeof(Mark),
"Profile array");
if (aprof == NULL)
exit (1);
mprof = aprof + (pmax+2);
pprof = mprof + pmax;
mark = ((Mark *) (pprof + pmax)) + 1;
Fetch_Profile(AP,p,pmax,aprof);
}
Fetch_Profile(MP,p,pmax,mprof);
Fetch_Profile(PP,p,pmax,pprof);
aprof[plen] = 0;
aprof[plen+1] = 1;
fprintf(fscf,"scaffold\t%s\t%lld\n",aroot,plen);
// For each contig, build stack of hap sites (= overlapping hap-mers), merging adjacent
// sites of the same polarity and then call process_blocks to finish the partitioning
// into putative phased blocks
eoc = 0;
end = 0;
frst = 0;
mtop = 0;
for (x = 0; x <= plen; x++)
{ int d;
if (aprof[x] == 0)
eoc = 1;
else
{ if (mprof[x] > 0)
d = 1;
else if (pprof[x] > 0)
d = -1;
else
continue;
if (x < end)
{ mrk += d;
end = x+KMER;
sum += 1;
continue;
}
}
if (end > 0 && abs(mrk) >= (sum+3)/4)
{ if (mtop > 0 && (mrk < 0) == (mark[mtop-1].mrk < 0))
{ mark[mtop-1].end = end;
if (mrk < 0)
mark[mtop-1].mrk += (sum+mrk)/2 - (end-beg);
else
mark[mtop-1].mrk += (end-beg) - (sum-mrk)/2;
}
else
{ mark[mtop].beg = beg;
mark[mtop].end = end;
mark[mtop].opp = 0;
if (mrk < 0)
mark[mtop].mrk = (sum+mrk)/2 - (end-beg);
else
mark[mtop].mrk = (end-beg) - (sum-mrk)/2;
mtop += 1;
}
}
if (eoc)
{ int ns, to, len;
if (mtop > 0)
{ nctg += 1;
fprintf(fctg,"contig\t%s\t%d\n",aroot,(x-frst)+(KMER-1));
mtop = merge_blocks(mtop,mark);
mark[0].beg = frst;
mark[mtop-1].end = x + (KMER-1);
for (i = 0; i < mtop; i++)
{ len = mark[i].end - mark[i].beg;
if (mark[i].mrk > 0)
{ ns = -mark[i].opp;
to = ns + mark[i].mrk;
fprintf(bed,"%d\t%d\t%d\t%s\t%.3f\t%d\t%d\n",
nctg,mark[i].beg,mark[i].end,mroot,(100.*ns)/to,ns,to);
fprintf(plot,"%s\t%d\t%d\t%d\t%d\n",mroot,NBLK+i,to-ns,ns,len);
fprintf(fblk,"block\t%s\t%d\n",mroot,len);
}
else
{ ns = mark[i].opp;
to = ns - mark[i].mrk;
fprintf(bed,"%d\t%d\t%d\t%s\t%.3f\t%d\t%d\n",
nctg,mark[i].beg,mark[i].end,proot,(100.*ns)/to,ns,to);
fprintf(plot,"%s\t%d\t%d\t%d\t%d\n",proot,NBLK+i,ns,to-ns,len);
fprintf(fblk,"block\t%s\t%d\n",proot,len);
}
stot += ns;
mtot += to;
BTOT += len;
if (len > BMAX)
BMAX = len;
else if (len < BMIN)
BMIN = len;
}
NBLK += mtop;
}
while (aprof[x+1] == 0)
x += 1;
eoc = 0;
end = 0;
mtop = 0;
frst = x+1;
}
else
{ beg = x;
end = x+KMER;
mrk = d;
sum = 1;
}
}
}
fprintf(bed,"total\t-t-\t-\t%.3f\t%lld\t%lld\n",
(100.*stot)/mtot,stot,mtot);
fclose(plot);
fclose(bed);
fclose(fblk);
fclose(fctg);
fclose(fscf);
Free_Profiles(MP);
Free_Profiles(PP);
Free_Profiles(AP);
return (nctg != nscf);
}
static void block_stats(char *aroot, char *out, char *troot)
{ FILE *sfile, *nfile;
int bn50;
int64 sum, thr;
nfile = fopen(Catenate(troot,".block.sizes","",""),"r");
sum = 0;
thr = BTOT/2;
while (fscanf(nfile,"block\t%*s\t%d\n",&bn50) == 1)
{ sum += bn50;
if (sum >= thr)
break;
}
fclose(nfile);
sfile = fopen(Catenate(out,".",aroot,".phased_block.stats"),"w");
fprintf(sfile,"# Blocks\tSum\tMin.\tAvg.\tN50\tMax.\n");
fprintf(sfile,"%d\t%lld\t%d\t%lld\t%d\t%d\n",NBLK,BTOT,BMIN,BTOT/NBLK,bn50,BMAX);
fclose(sfile);
}
/****************************************************************************************
*
* Main Routine
*
*****************************************************************************************/
static int check_table(char *name, int lmer)
{ int kmer;
FILE *f;
f = fopen(name,"r");
if (f == NULL)
{ fprintf(stderr,"\n%s: Cannot find FastK table %s\n",Prog_Name,name);
exit (1);
}
else
{ fread(&kmer,sizeof(int),1,f);
if (lmer != 0 && kmer != lmer)
{ fprintf(stderr,"\n%s: Kmer (%d) of table %s != %d\n",Prog_Name,kmer,name,lmer);
exit (1);
}
fclose(f);
return (kmer);
}
}
int main(int argc, char *argv[])
{ char *READS, *ASM[2], *MAT, *PAT, *OUT;
char *RROOT, *AROOT[2], *MROOT, *PROOT;
char *ATAB[2], *APRF[2], *MPRF[2], *PPRF[2], *troot;
int KEEP;
int LINE, FILL, STACK;
int PDF;
int ZGRAM;
double XDIM, YDIM;
double XREL, YREL;
int XMAX;
int64 YMAX;
int NTHREADS;
char *SORT_PATH;
char command[5000];
// Command line processing
{ int i, j, k;
int flags[128];
char *eptr;
(void) eptr;
ARG_INIT("MerquryFK");
XDIM = 6.0; // Plot width & height (in inches)
YDIM = 4.5;
XREL = 2.1; // Peak relative x,y scale
YREL = 1.1;
XMAX = 0; // 0 => use relative x,y above
YMAX = 0;
PDF = 0;
NTHREADS = 4;
SORT_PATH = "/tmp";
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vlfszk")
break;
case 'h':
ARG_REAL(YDIM);
break;
case 'p':
if (strcmp("df",argv[i]+2) == 0)
PDF = 1;
else
{ fprintf(stderr,"%s: don't recognize option %s\n",Prog_Name,argv[i]);
exit (1);
}
break;
case 'w':
ARG_REAL(XDIM);
break;
case 'x':
ARG_REAL(XREL);
if (XREL <= 0.)
{ fprintf(stderr,"%s: max x scaling factor must be > 0\n",Prog_Name);
exit (1);
}
break;
case 'y':
ARG_REAL(YREL);
if (YREL <= 0.)
{ fprintf(stderr,"%s: max y scaling factor must be > 0\n",Prog_Name);
exit (1);
}
break;
case 'P':
SORT_PATH = argv[i]+2;
break;
case 'T':
ARG_POSITIVE(NTHREADS,"Number of threads")
break;
case 'X':
ARG_POSITIVE(XMAX,"x max");
break;
case 'Y':
{ int ymax;
ARG_POSITIVE(ymax,"y max");
YMAX = ymax;
break;
}
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
LINE = flags['l'];
FILL = flags['f'];
STACK = flags['s'];
ZGRAM = flags['z'];
KEEP = flags['k'];
if (argc < 4 || argc > 7)
{ fprintf(stderr,"\nUsage: %s %s\n",Prog_Name,Usage[0]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[1]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[2]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[3]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[4]);
fprintf(stderr,"\n");
fprintf(stderr," -w: width in inches of plots\n");
fprintf(stderr," -h: height in inches of plots\n");
fprintf(stderr," -x: max x as a real-valued multiple of x* with max\n");
fprintf(stderr," count 'peak' away from the origin\n");
fprintf(stderr," -X: max x as an int value in absolute terms\n");
fprintf(stderr," -y: max y as a real-valued multiple of max count\n");
fprintf(stderr," 'peak' away from the origin\n");
fprintf(stderr," -Y: max y as an int value in absolute terms\n");
fprintf(stderr,"\n");
fprintf(stderr," -l: draw line plot\n");
fprintf(stderr," -f: draw fill plot\n");
fprintf(stderr," -s: draw stack plot\n");
fprintf(stderr," any combo allowed, none => draw all\n");
fprintf(stderr,"\n");
fprintf(stderr," -z: plot counts of k-mers unique to assembly\n");
fprintf(stderr,"\n");
fprintf(stderr," -pdf: output .pdf (default is .png)\n");
fprintf(stderr,"\n");
fprintf(stderr," -v: verbose output to stderr\n");
fprintf(stderr," -k: keep plotting data as .cni, .asmi, and .hpi files\n");
fprintf(stderr," -T: number of threads to use\n");
fprintf(stderr," -P: Place all temporary files in directory -P.\n");
exit (1);
}
if (LINE+FILL+STACK == 0)
LINE = FILL = STACK = 1;
READS = argv[1];
switch (argc)
{ case 4:
if (VERBOSE)
fprintf(stderr,"\n Single diploid assembly, no trio data\n");
MAT = NULL;
ASM[0] = argv[2];
ASM[1] = NULL;
break;
case 5:
if (VERBOSE)
fprintf(stderr,"\n Two haploid assemblies, no trio data\n");
MAT = NULL;
ASM[0] = argv[2];
ASM[1] = argv[3];
break;
case 6:
if (VERBOSE)
fprintf(stderr,"\n Single diploid assembly with trio data\n");
MAT = argv[2];
PAT = argv[3];
ASM[0] = argv[4];
ASM[1] = NULL;
break;
case 7:
if (VERBOSE)
fprintf(stderr,"\n Two haploid assemblies with trio data\n");
MAT = argv[2];
PAT = argv[3];
ASM[0] = argv[4];
ASM[1] = argv[5];
break;
}
OUT = argv[argc-1];
// Remove any suffixes from argument names
{ char *suffix[10] = { ".gz", ".fa", ".fq", ".fasta", ".fastq", ".db",
".dam", ".sam", ".bam", ".cram" };
troot = mktemp(template);
READS = PathnRoot(READS,".ktab");
RROOT = Root(READS,"");
if (MAT != NULL)
{ char *x;
x = PathnRoot(MAT,".ktab");
MAT = PathnRoot(x,".hap");
free(x);
x = PathnRoot(PAT,".ktab");
PAT = PathnRoot(x,".hap");
free(x);
MROOT = Root(MAT,"");
PROOT = Root(PAT,"");
if (strcmp(MROOT,PROOT) == 0)
{ fprintf(stderr,"%s: Parent haplotype tables have the same root name %s\n",
Prog_Name,MROOT);
exit (1);
}
}
for (i = 0; i < 2; i++)
{ char *A = ASM[i];
int len;
if (A == NULL)
{ AROOT[i] = NULL;
continue;
}
for (j = 0; j < 10; j++)
{ len = strlen(A) - strlen(suffix[j]);
if (strcmp(A+len,suffix[j]) == 0)
A[len] = '\0';
}
AROOT[i] = Root(A,"");
}
if (ASM[1] != NULL && strcmp(AROOT[0],AROOT[1]) == 0)
{ fprintf(stderr,"%s: Two assemblies have the same root name %s\n",Prog_Name,AROOT[0]);
exit (1);
}
KMER = check_table(Catenate(READS,".ktab","",""),0);
if (MAT != NULL)
{ KMER = check_table(Catenate(MAT,".hap",".ktab",""),KMER);
KMER = check_table(Catenate(PAT,".hap",".ktab",""),KMER);
}
if (VERBOSE)
fprintf(stderr,"\n Kmer size is %d\n",KMER);
ANCHOR_MARK *= KMER;
}
}
// Non-Trio action ...
{ char Out[1000];
char A1uA2[1000];
char Hname[1000];
Histogram *Rhist;
int i, k;
// Load read histogram and infer SOLID threshold and count
Rhist = Load_Histogram(READS);
if (Rhist == NULL)
{ fprintf(stderr,"\n%s: Cannot find FastK histograam %s.hist\n",Prog_Name,READS);
exit (1);
}
if (KMER != Rhist->kmer)
{ fprintf(stderr,"\n%s: Kmer size of %s.hist doesn't match %s.ktab\n",Prog_Name,READS,READS);
exit (1);
}
Modify_Histogram(Rhist,Rhist->low,Rhist->high,1);
{ int low = Rhist->low;
int high = Rhist->high;
int64 *hist = Rhist->hist;
for (k = low+1; hist[k] < hist[k-1]; k++)
if (k >= high)
break;
SOLID_THRESH = k;
SOLID_COUNT = 0;
while (k <= high)
SOLID_COUNT += hist[k++];
if (VERBOSE)
fprintf(stderr,"\n Solid k-mer cutoff is %d\n",SOLID_THRESH);
}
Free_Histogram(Rhist);
// For each assembly
{ FILE *qvs;
int64 *summary, totl, miss;
qvs = fopen(Catenate(OUT,"","",".qv"),"w");
fprintf(qvs,"Assembly\tNo Support\tTotal\tError %%\tQV\n");
for (i = 0; i < 2; i++)
{ char *A = ASM[i];
char *R = AROOT[i];
double err, qv;
if (A == NULL)
continue;
// Create assembly tables and profiles
ATAB[i] = mktemp(templateA[i]);
APRF[i] = mktemp(templateR[i]);
sprintf(command,"FastK -k%d -T%d -P%s -t1 -p %s -N%s",
KMER,NTHREADS,SORT_PATH,A,ATAB[i]);
SystemX(command);
sprintf(command,"FastK -k%d -T%d -P%s -p:%s %s -N%s",
KMER,NTHREADS,SORT_PATH,READS,A,APRF[i]);
SystemX(command);
// Make a CN-spectra plot
if (VERBOSE)
fprintf(stderr,"\n Making CN-spectra plot for assembly %s\n",R);
sprintf(Out,"%s.%s.spectra-cn",OUT,R);
cn_plot(Out,KEEP,ATAB[i],READS,
XDIM,YDIM,XREL,YREL,XMAX,YMAX,PDF,ZGRAM,
LINE,FILL,STACK,NTHREADS);
// Compute scaffold QV's and make bed file
summary = scan_asm(ATAB[i],APRF[i],R,RROOT,OUT);
// Output global qv
err = 1. - pow(1.-(1.*summary[0])/summary[1],1./KMER);
qv = -10.*log10(err);
fprintf(qvs,"%s\t%lld\t%lld\t%.4f\t%.1f\n",R,summary[0],summary[1],100.*err,qv);
if (i == 0)
{ miss = summary[0];
totl = summary[1];
}
else
{ miss += summary[0];
totl += summary[1];
err = 1. - pow(1.-(1.*miss)/totl,1./KMER);
qv = -10.*log10(err);
fprintf(qvs,"both\t%lld\t%lld\t%.4f\t%.1f\n",miss,totl,100.*err,qv);
}
}
fclose(qvs);
}
// 1 diploid assembly ...
if (ASM[1] == NULL)
{ Histogram *H;
FILE *cps;
// Compute & output completeness stat
if (VERBOSE)
fprintf(stderr,"\n Computing completeness stats for assembly %s\n",AROOT[0]);
sprintf(command,"Logex -H1 -T%d '%s.0 = A-B[%d-]' %s %s",
NTHREADS,troot,SOLID_THRESH,ATAB[0],READS);
SystemX(command);
cps = fopen(Catenate(OUT,"","",".completeness.stats"),"a");
fprintf(cps,"Assembly\tRegion\tFound\tTotal\t%% Covered\n");
sprintf(Hname,"%s.0",troot);
H = Load_Histogram(Hname);
fprintf(cps,"%s\tall\t%lld\t%lld\t%.2f\n",AROOT[0],(SOLID_COUNT-H->hist[1]),SOLID_COUNT,
(SOLID_COUNT-H->hist[1])/(.01*SOLID_COUNT));
Free_Histogram(H);
fclose(cps);
sprintf(command,"Fastrm %s.0.hist",troot);
SystemX(command);
// Produce assembly-spectra plots
if (VERBOSE)
fprintf(stderr,"\n Making Assembly-spectra plot for assembly %s\n",AROOT[0]);
sprintf(Out,"%s.spectra-asm",OUT);
asm_plot(Out,KEEP,ASM,ATAB,READS,
XDIM,YDIM,XREL,YREL,XMAX,YMAX,PDF,ZGRAM,
LINE,FILL,STACK,NTHREADS);
}
// 2 haploid assemblies ...
else
{ Histogram *H;
FILE *cps;
if (VERBOSE)
fprintf(stderr,"\n Making CN-spectra plot for %s U %s\n",AROOT[0],AROOT[1]);
// Form the "k-mer union" of the two assemblies
sprintf(A1uA2,"%s.U",troot);
sprintf(command,"Logex -T%d '%s = A|+B' %s %s",NTHREADS,A1uA2,ATAB[0],ATAB[1]);
SystemX(command);
// Make a CN spectra plot for the union
sprintf(Out,"%s.spectra-cn",OUT);
cn_plot(Out,KEEP,A1uA2,READS,
XDIM,YDIM,XREL,YREL,XMAX,YMAX,PDF,ZGRAM,
LINE,FILL,STACK,NTHREADS);
// Compute & output completeness stats
if (VERBOSE)
fprintf(stderr,"\n Computing completeness stats for %s and %s\n",AROOT[0],AROOT[1]);
sprintf(command,
"Logex -H1 -T%d '%s.0 = A&.D[%d-]' '%s.1=B&.D[%d-]' '%s.2=C&.D[%d-]' %s %s %s %s",
NTHREADS,troot,SOLID_THRESH,troot,SOLID_THRESH,troot,SOLID_THRESH,
ATAB[0],ATAB[1],A1uA2,READS);
SystemX(command);
cps = fopen(Catenate(OUT,"","",".completeness.stats"),"a");
fprintf(cps,"Assembly\tRegion\tFound\tTotal\t%% Covered\n");
sprintf(Hname,"%s.0",troot);
H = Load_Histogram(Hname);
fprintf(cps,"%s\tall\t%lld\t%lld\t%.2f\n",AROOT[0],H->hist[1],SOLID_COUNT,
H->hist[1]/(.01*SOLID_COUNT));
Free_Histogram(H);
sprintf(Hname,"%s.1",troot);
H = Load_Histogram(Hname);
fprintf(cps,"%s\tall\t%lld\t%lld\t%.2f\n",AROOT[1],H->hist[1],SOLID_COUNT,
H->hist[1]/(.01*SOLID_COUNT));
Free_Histogram(H);
sprintf(Hname,"%s.2",troot);
H = Load_Histogram(Hname);