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ALNplot.c
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/*********************************************************************************
* MIT License *
* *
* Copyright (c) 2024 Chenxi Zhou <[email protected]> *
* *
* 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. *
*********************************************************************************/
/*****************************************************************************************\
* *
* Genome Alignment Plotter *
* *
* Author: Chenxi Zhou (with an assist from Gene Myers) *
* Date : June 2024 *
* *
\*****************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include <ctype.h>
#include <unistd.h>
#include <pthread.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <zlib.h>
#include "GDB.h"
#include "hash.h"
#include "select.h"
#include "alncode.h"
#undef DEBUG_MAKE_HASH
#undef DEBUG_READ_1ALN
#undef DEBUG_AXIS_CONF
#define MAX_XY_LEN 10000 // Max/Min plotting width/height
#define MIN_XY_LEN 100
#define MAX_LAB_LEN 20 // Max number characters for sequence names
#define MAX_LAB_FRC .2 // Max ratio of label to line plot panel
// Command line syntax and global parameter variables
static char *Usage[] =
{ "[-vSL] [-T<int(4)>] [-p[:<output:path>[.pdf]]]",
"[-l<int(100)>] [-i<float(.7)>] [-n<int(100000)>]",
"[-H<int(600)>] [-W<int>] [-f<int>] [-t<float>]",
"<alignment:path>[.1aln|.paf[.gz]]> [<selection>|<FILE> [<selection>|<FILE>]]",
};
static int VERBOSE; // -v
// static int HIGHLIGHT; // -h
// static int TRYADIAG; // -d
static int PRINTSID; // -S
static int LABELS; // ! -L
static int NTHREADS = 4; // -T
static char *OUTEPS = NULL; // -p
static int MINALEN = 100; // -a
static double MINAIDNT = 0.7; // -e
static int MAXALIGN = 100000; // -n
static int IMGHEIGH = 0; // -H
static int IMGWIDTH = 0; // -W
static int FONTSIZE = 0; // -f
static double LINESIZE = 0; // -t
// Array of segments to plot
typedef struct
{ uint8 flag;
int aread, bread;
int abpos, bbpos;
int aepos, bepos;
// int group; // segment group - e.g. chain
} Segment;
#define DEL_FLAG 0x1
#define COL_GRAY 0x2
#define COL_RED 0x4
#define COL_BLUE 0x8
#define IS_DEL(flag) ((flag)&DEL_FLAG)
#define SET_DEL(flag) ((flag)|=DEL_FLAG)
#define IS_COLOR(flag) ((flag)&0xE)
#define IS_RED(flag) ((flag)&COL_RED)
#define IS_BLUE(flag) ((flag)&COL_BLUE)
#define IS_GRAY(flag) ((flag)&COL_GRAY)
#define UNSET_COLOR(flag) ((flag)&=0xF1)
#define SET_RED(flag) (UNSET_COLOR(flag), (flag)|=COL_RED)
#define SET_BLUE(flag) (UNSET_COLOR(flag), (flag)|=COL_BLUE)
#define SET_GRAY(flag) (UNSET_COLOR(flag), (flag)|=COL_GRAY)
static Segment *segments = NULL;
static int64 nSegment = 0;
// Genome skeletons and auxiliary info
static int ISTWO; // If two GDBs are different
static GDB _AGDB, *AGDB = &_AGDB; // 1st genome skeleton with parts ...
static GDB _BGDB, *BGDB = &_BGDB; // 2nd genome skeleton with parts ...
static int NASCAFF; // Number scaffolds
static int NACONTIG; // Number contigs
static GDB_SCAFFOLD *ASCAFFS; // Scaffold record array
static GDB_CONTIG *ACONTIG; // Contig record array
static int NBSCAFF; // Number scaffolds
static int NBCONTIG; // Number contigs
static GDB_SCAFFOLD *BSCAFFS; // Scaffold record array
static GDB_CONTIG *BCONTIG; // Contig record array
static Hash_Table *AHASH; // Scaffold names hash table
static Hash_Table *BHASH; // Scaffold names hash table
static Contig_Range *ACHORD; // [0..NACONTIG) Portion of each contig to plot (or not)
static Contig_Range *BCHORD; // [0..NBCONTIG) Portion of each contig to plot (or not)
// Threading communication packet (read_1aln_block & aln_clip)
typedef struct
{ int64 beg;
int64 end;
OneFile *in;
Segment *segs;
int64 nseg;
GDB_CONTIG *bctg;
} Packet;
// Helvetica font character width
static double HELVETICA[128] =
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,
0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000,
0.278, 0.278, 0.355, 0.556, 0.556, 0.889, 0.667, 0.222, 0.333, 0.333, 0.389, 0.584, 0.278, 0.333, 0.278, 0.278,
0.556, 0.556, 0.556, 0.556, 0.556, 0.556, 0.556, 0.556, 0.556, 0.556, 0.278, 0.278, 0.584, 0.584, 0.584, 0.556,
1.015, 0.667, 0.667, 0.722, 0.722, 0.667, 0.611, 0.778, 0.722, 0.278, 0.500, 0.667, 0.556, 0.833, 0.722, 0.778,
0.667, 0.778, 0.722, 0.667, 0.611, 0.722, 0.667, 0.944, 0.667, 0.667, 0.611, 0.278, 0.278, 0.278, 0.469, 0.556,
0.222, 0.556, 0.556, 0.500, 0.556, 0.556, 0.278, 0.556, 0.556, 0.222, 0.222, 0.500, 0.222, 0.833, 0.556, 0.556,
0.556, 0.556, 0.333, 0.500, 0.278, 0.556, 0.500, 0.722, 0.500, 0.500, 0.500, 0.334, 0.260, 0.334, 0.584, 0.000
};
/*******************************************************************************************
*
* Utilities
*
*******************************************************************************************/
static char *PDFTOOLS[4] = {"pstopdf", "epstopdf", "ps2pdf", "eps2pdf"};
int run_system_cmd(char *cmd, int retry)
{ int exit_code = system(cmd);
--retry;
if ((exit_code != -1 && !WEXITSTATUS(exit_code)) || !retry)
return (exit_code);
return (run_system_cmd(cmd, retry));
}
int check_executable(char *exe)
{ char cmd[4096];
int exit_code;
sprintf(cmd, "which %s 1>/dev/null 2>/dev/null", exe);
exit_code = run_system_cmd(cmd, 1);
if (exit_code == -1 || WEXITSTATUS(exit_code))
return (0);
return (1);
}
char *findPDFtool()
{ uint64 i;
for (i = 0; i < sizeof(PDFTOOLS) / sizeof(char *); i++)
if (check_executable(PDFTOOLS[i]))
return (PDFTOOLS[i]);
return (NULL);
}
static inline void expandBuffer(char **names, uint32 *n, uint32 *m, uint32 l)
{ if (*n + l > *m)
{ *m <<= 1;
*names = (char *)Realloc(*names,sizeof(char)*(*m),"Reallocating name array");
if (*names == NULL)
exit (1);
}
}
// Read next line into a buffer and return a pointer to the buffer
// the length of the line. NB: replaces '\n' with '\0'.
static char *read_line(void *input, int gzipd, int nline, char *spath)
{ static char *buffer;
static int bmax = 0;
int len;
if (bmax == 0)
{ bmax = 500;
buffer = (char *) malloc(bmax);
if (buffer == NULL)
{ fprintf(stderr,"%s: Out of memory reading %s\n",Prog_Name,spath);
exit (1);
}
}
if (gzipd)
{ if (gzgets(input,buffer,bmax) == NULL)
{ if (gzeof(input))
{ free(buffer);
bmax = 0;
return (NULL);
}
fprintf(stderr,"%s: Could not read next line, %d, of file %s\n",Prog_Name,nline,spath);
exit (1);
}
}
else
{ if (fgets(buffer,bmax,input) == NULL)
{ if (feof(input))
{ free(buffer);
bmax = 0;
return (NULL);
}
fprintf(stderr,"%s: Could not read next line, %d, of file %s\n",Prog_Name,nline,spath);
exit (1);
}
}
len = strlen(buffer);
while (buffer[len-1] != '\n')
{ bmax = ((int) (1.4*bmax)) + 100;
buffer = (char *) realloc(buffer,bmax);
if (buffer == NULL)
{ fprintf(stderr,"%s: Out of memory reading %s\n",Prog_Name,spath);
exit (1);
}
if (gzipd)
{ if (gzgets(input,buffer+len,bmax-len) == NULL)
{ if (gzeof(input))
fprintf(stderr,"%s: Last line %d of file %s does not end with new-line\n",
Prog_Name,nline,spath);
else
fprintf(stderr,"%s: Could not read next line, %d, of file %s\n",
Prog_Name,nline,spath);
exit (1);
}
}
else
{ if (fgets(buffer+len,bmax-len,input) == NULL)
{ if (feof(input))
fprintf(stderr,"%s: Last line %d of file %s does not end with new-line\n",
Prog_Name,nline,spath);
else
fprintf(stderr,"%s: Could not read next line, %d, of file %s\n",
Prog_Name,nline,spath);
exit (1);
}
}
len += strlen(buffer+len);
}
buffer[--len] = '\0';
return (buffer);
}
/*******************************************************************************************
*
* Read .1aln file creating array of segments and two GDB skeletons, AGDB & BGDB,
* and hash tables, AHASH & BHASH, of the scaffold names for each.
*
*******************************************************************************************/
void *read_1aln_block(void *args)
{ Packet *parm = (Packet *) args;
int64 beg = parm->beg;
int64 end = parm->end;
GDB_CONTIG *bctg = parm->bctg;
OneFile *in = parm->in;
Segment *segs = parm->segs;
int64 nseg = 0;
// int ngroup;
// For each alignment do
if (!oneGoto (parm->in, 'A', beg+1))
{ fprintf(stderr,"%s: Could not locate to object %lld in 1aln file\n",Prog_Name,beg+1);
exit (1);
}
oneReadLine(parm->in);
// Get the group id of the first alignment
// ngroup = -1; // oneGetGroup (parm->in, beg);
// if (ngroup < 0) ngroup = 0;
{ int64 i;
uint32 flags;
uint8 flag;
int aread, bread;
int abpos, bbpos;
int aepos, bepos;
// int group;
int diffs;
int blocksum, iid;
// Set group to be the first
// group = ngroup;
for (i = beg; i < end; i++)
{ // read i-th alignment record
if (in->lineType != 'A')
{ fprintf(stderr,"%s: Failed to be at start of alignment\n",Prog_Name);
exit (1);
}
flags = 0;
aread = oneInt(in,0);
abpos = oneInt(in,1);
aepos = oneInt(in,2);
bread = oneInt(in,3);
bbpos = oneInt(in,4);
bepos = oneInt(in,5);
diffs = 0;
while (oneReadLine(in))
if (in->lineType == 'R')
flags |= COMP_FLAG;
else if (in->lineType == 'D')
diffs = oneInt(in,0);
else if (in->lineType == 'A')
break; // stop at next A-line
else
continue; // skip trace lines
if (aepos - abpos < MINALEN || bepos - bbpos < MINALEN)
continue; // filter by segment size
blocksum = (aepos-abpos) + (bepos-bbpos);
iid = (blocksum - diffs) / 2;
if (2.*iid / blocksum < MINAIDNT)
continue; // filter by segment identity
flag = 0;
if (COMP(flags))
{ bbpos = bctg[bread].clen - bbpos;
bepos = bctg[bread].clen - bepos;
}
// add to output
segs->flag = flag;
segs->aread = aread;
segs->abpos = abpos;
segs->aepos = aepos;
segs->bread = bread;
segs->bbpos = bbpos;
segs->bepos = bepos;
// segs->group = group;
segs += 1;
nseg += 1;
// change group after this alignment
// group = ngroup;
}
}
parm->nseg = nseg;
return (NULL);
}
void read_1aln(char *oneAlnFile)
{ OneFile *input;
int64 novl;
// Initiate .1aln file reading and read header information
{ char *cpath;
char *src1_name, *src2_name;
char *sptr, *eptr;
char *head;
int s, TSPACE;
input = open_Aln_Read(oneAlnFile,NTHREADS,&novl,&TSPACE,&src1_name,&src2_name,&cpath);
if (input == NULL)
{ fprintf(stderr,"%s: Could not open .1aln file: %s\n",Prog_Name,oneAlnFile);
exit (1);
}
ISTWO = (src2_name != NULL);
Get_GDB(AGDB,src1_name,cpath,0);
if (ISTWO)
Get_GDB(BGDB,src1_name,cpath,0);
else
BGDB = AGDB;
free(src1_name);
free(src2_name);
free(cpath);
NASCAFF = AGDB->nscaff;
NACONTIG = AGDB->ncontig;
ASCAFFS = AGDB->scaffolds;
ACONTIG = AGDB->contigs;
NBSCAFF = BGDB->nscaff;
NBCONTIG = BGDB->ncontig;
BSCAFFS = BGDB->scaffolds;
BCONTIG = BGDB->contigs;
AHASH = New_Hash_Table(NASCAFF,0);
head = AGDB->headers;
for (s = 0; s < NASCAFF; s++)
{ sptr = head + ASCAFFS[s].hoff;
for (eptr = sptr; *eptr != '\0'; eptr++)
if (isspace(*eptr))
break;
*eptr = '\0';
if (Hash_Lookup(AHASH,sptr) < 0)
Hash_Add(AHASH,sptr);
else
{ fprintf(stderr,"%s: Duplicate scaffold name: %s\n",Prog_Name,sptr);
exit (1);
}
}
if (ISTWO)
{ BHASH = New_Hash_Table(NBSCAFF,0);
head = BGDB->headers;
for (s = 0; s < NBSCAFF; s++)
{ sptr = head + BSCAFFS[s].hoff;
for (eptr = sptr; *eptr != '\0'; eptr++)
if (isspace(*eptr))
break;
*eptr = '\0';
if (Hash_Lookup(BHASH,sptr) < 0)
Hash_Add(BHASH,sptr);
else
{ fprintf(stderr,"%s: Duplicate scaffold name: %s\n",Prog_Name,sptr);
exit (1);
}
}
}
else
BHASH = AHASH;
}
#ifdef DEBUG_MAKE_HASH
{ int i;
fprintf(stderr,"%s: DB_A\n",Prog_Name);
fprintf(stderr,"%s: List of contigs (NACTG=%d)\n",Prog_Name,NACONTIG);
fprintf(stderr,"%s: INDEX SCAF OFFSET LENGTH\n",Prog_Name);
for (i = 0; i < NACONTIG; i++)
fprintf(stderr,"%s: %6d %6d %10lld %10lld\n",Prog_Name,i,
ACONTIG[i].scaf,ACONTIG[i].sbeg,ACONTIG[i].clen);
fprintf(stderr,"%s: List of scaffolds (NASCAFF=%d)\n",Prog_Name,NASCAFF);
for (i = 0; i < NASCAFF; i++)
fprintf(stderr,"%s: %6d %s\n",Prog_Name,i,Get_Hash_String(AHASH,i));
if (ISTWO)
{ fprintf(stderr,"%s: DB_B\n",Prog_Name);
fprintf(stderr,"%s: List of contigs (NBCTG=%d)\n",Prog_Name,NBCONTIG);
fprintf(stderr,"%s: INDEX SCAF OFFSET LENGTH\n",Prog_Name);
for (i = 0; i < NBCONTIG; i++)
fprintf(stderr,"%s: %6d %6d %10lld %10lld\n",Prog_Name,i,
BCONTIG[i].scaf,BCONTIG[i].sbeg,BCONTIG[i].clen);
fprintf(stderr,"%s: List of scaffolds (NBSCAFF=%d)\n",Prog_Name,NBSCAFF);
for (i = 0; i < NBSCAFF; i++)
fprintf(stderr,"%s: %6d %s\n",Prog_Name,i,Get_Hash_String(BHASH,i));
}
}
#endif
// Read alignment segments
{ int p;
Packet parm[NTHREADS];
pthread_t threads[NTHREADS];
// Divide .1aln into NTHREADS parts
segments = (Segment *) Malloc(sizeof(Segment)*novl, "Allocating segment array");
for (p = 0; p < NTHREADS ; p++)
{ parm[p].beg = (p * novl) / NTHREADS;
if (p > 0)
parm[p-1].end = parm[p].beg;
parm[p].segs = segments + parm[p].beg;
parm[p].nseg = 0;
parm[p].in = input + p;
parm[p].bctg = BGDB->contigs;
}
parm[NTHREADS-1].end = novl;
// Use NTHREADS to produce alignment segments for each part
for (p = 1; p < NTHREADS; p++)
pthread_create(threads+p,NULL,read_1aln_block,parm+p);
read_1aln_block(parm);
for (p = 1; p < NTHREADS; p++)
pthread_join(threads[p],NULL);
// Collect results from different part
nSegment = parm[0].nseg;
for (p = 1; p < NTHREADS; p++)
{ if (nSegment < parm[p].beg)
memmove(segments+nSegment,parm[p].segs,sizeof(Segment)*parm[p].nseg);
nSegment += parm[p].nseg;
}
if (nSegment < novl)
segments = Realloc(segments,sizeof(Segment)*nSegment,"Compacting segment arrary");
#ifdef DEBUG_READ_1ALN
fprintf(stderr, "%s: %9lld segments loaded\n",Prog_Name,novl);
fprintf(stderr, "%s: %9lld after filtering\n",Prog_Name,nSegment);
#endif
}
oneFileClose(input);
}
/*******************************************************************************************
*
* Read .paf file creating array of segments and two GDB skeletons, AGDB & BGDB
* and hash tables, AHASH & BHASH, of the scaffold names for each.
*
*******************************************************************************************/
void read_paf(char *pafAlnFile, int gzipd)
{ void *input;
int nline;
int i, naseq, maseq, nbseq, mbseq;
int index;
uint64 nsegs, msegs;
Segment *segs;
char *fptrs[11], *fptr, *eptr;
char *head;
int alen, blen, *alens, *blens;;
int aread, bread;
int abpos, bbpos;
int aepos, bepos;
// int group;
int blocksum, iid;
uint8 flag;
if (gzipd)
input = gzopen(pafAlnFile,"r");
else
input = fopen(pafAlnFile,"r");
AHASH = New_Hash_Table(1024,1);
BHASH = New_Hash_Table(1024,1);
naseq = 0;
maseq = 1024;
nbseq = 0;
mbseq = 1024;
nsegs = 0;
msegs = 4096;
alens = (int *) Malloc(sizeof(int) * maseq, "Allocating length map");
blens = (int *) Malloc(sizeof(int) * mbseq, "Allocating length map");
segments = (Segment *) Malloc(sizeof(Segment) * msegs, "Allocating segment array");
segs = segments;
nline = 1;
while ((eptr = read_line(input,gzipd,nline++,pafAlnFile)) != NULL)
{
fptr = eptr; // parse PAF line
for (i = 0; i < 11; i++)
{ while (*eptr != '\t' && *eptr != '\n' && *eptr != '\0')
eptr++;
if (eptr > fptr)
fptrs[i] = fptr;
if (*eptr == '\t')
{ *eptr = '\0';
fptr = ++eptr;
}
else
{ *eptr = '\0';
*fptr = '\0';
break;
}
}
if (i != 11)
continue;
index = Hash_Lookup(AHASH, fptrs[0]);
alen = strtol(fptrs[1], &eptr, 10);
if (index < 0)
{ alens[naseq++] = alen;
if (naseq == maseq)
{ maseq <<= 1;
alens = (int *) Realloc(alens, sizeof(int) * maseq, "Reallocating length map");
}
index = Hash_Add(AHASH, fptrs[0]);
}
aread = index;
abpos = strtol(fptrs[2], &eptr, 10);
aepos = strtol(fptrs[3], &eptr, 10);
index = Hash_Lookup(BHASH, fptrs[5]);
blen = strtol(fptrs[6], &eptr, 10);
if (index < 0)
{ blens[nbseq++] = blen;
if (nbseq == mbseq)
{ mbseq <<= 1;
blens = (int *) Realloc(blens, sizeof(int) * mbseq, "Reallocating length map");
}
index = Hash_Add(BHASH, fptrs[5]);
}
bread = index;
bbpos = strtol(fptrs[7], &eptr, 10);
bepos = strtol(fptrs[8], &eptr, 10);
if (aepos - abpos < MINALEN || bepos - bbpos < MINALEN) // filter by segment size
continue;
blocksum = (aepos-abpos) + (bepos-bbpos);
iid = strtol(fptrs[9], &eptr, 10);
if (2.*iid / blocksum < MINAIDNT) // filter by segment identity
continue;
/***
group = 0; // parse 'cn:i' tag to find segment group if exists
while (fptr)
{ eptr = fptr;
while (*eptr != '\t' && *eptr != '\n' && *eptr != '\0')
eptr++;
if (eptr - fptr > 5 && !strncmp(fptr, "cn:i:", 5))
{ group = strtol(fptr + 5, 0, 10);
break;
}
if (*eptr != '\t')
break;
fptr = ++eptr;
}
**/
flag = 0; // Add to segment array
if (*fptrs[4] == '-')
{ int tmp = bbpos;
bbpos = bepos;
bepos = tmp;
}
segs->flag = flag;
segs->aread = aread;
segs->bread = bread;
segs->abpos = abpos;
segs->aepos = aepos;
segs->bbpos = bbpos;
segs->bepos = bepos;
// segs->group = group;
nsegs += 1;
if (nsegs == msegs)
{ msegs <<= 1;
segments = (Segment *) Realloc(segments, sizeof(Segment) * msegs,
"Reallocating segment array");
}
segs = segments + nsegs;
}
if (gzipd)
gzclose(input);
else
fclose(input);
ISTWO = 1;
nSegment = nsegs;
// Contigs = Scaffolds so the underlying GDB is ...
AGDB->nscaff = AGDB->ncontig = NASCAFF = NACONTIG = naseq;
BGDB->nscaff = BGDB->ncontig = NBSCAFF = NBCONTIG = nbseq;
AGDB->scaffolds = ASCAFFS = Malloc(sizeof(GDB_SCAFFOLD)*(NASCAFF+NBSCAFF),"Allocating scaffolds");
AGDB->contigs = ACONTIG = Malloc(sizeof(GDB_CONTIG)*(NACONTIG+NBCONTIG),"Allocating contigs");
AGDB->headers = Get_Hash_String(AHASH,0);
BGDB->scaffolds = BSCAFFS = ASCAFFS + NASCAFF;
BGDB->contigs = BCONTIG = ACONTIG + NACONTIG;
BGDB->headers = Get_Hash_String(BHASH,0);
head = AGDB->headers;
for (i = 0; i < NASCAFF; i++)
{ ASCAFFS[i].slen = alens[i];
ASCAFFS[i].fctg = i;
ASCAFFS[i].ectg = i+1;
ASCAFFS[i].hoff = Get_Hash_String(AHASH,i) - head;
}
for (i = 0; i < NACONTIG; i++)
{ ACONTIG[i].clen = alens[i];
ACONTIG[i].sbeg = 0;
ACONTIG[i].boff = 0;
ACONTIG[i].scaf = i;
}
head = BGDB->headers;
for (i = 0; i < NBSCAFF; i++)
{ BSCAFFS[i].slen = blens[i];
BSCAFFS[i].fctg = i;
BSCAFFS[i].ectg = i+1;
BSCAFFS[i].hoff = Get_Hash_String(BHASH,i) - head;
}
for (i = 0; i < NBCONTIG; i++)
{ BCONTIG[i].clen = blens[i];
BCONTIG[i].sbeg = 0;
BCONTIG[i].boff = 0;
BCONTIG[i].scaf = i;
}
#ifdef DEBUG_MAKE_HASH
{ int i;
fprintf(stderr,"%s: DB_A\n",Prog_Name);
fprintf(stderr,"%s: List of contigs (NACTG=%d)\n",Prog_Name,NACONTIG);
fprintf(stderr,"%s: INDEX SCAF OFFSET LENGTH\n",Prog_Name);
for (i = 0; i < NACONTIG; i++)
fprintf(stderr,"%s: %6d %6d %10lld %10lld\n",Prog_Name,i,
ACONTIG[i].scaf,ACONTIG[i].sbeg,ACONTIG[i].clen);
fprintf(stderr,"%s: List of scaffolds (NASCAFF=%d)\n",Prog_Name,NASCAFF);
for (i = 0; i < NASCAFF; i++)
fprintf(stderr,"%s: %6d %s\n",Prog_Name,i,Get_Hash_String(AHASH,i));
if (ISTWO)
{ fprintf(stderr,"%s: DB_B\n",Prog_Name);
fprintf(stderr,"%s: List of contigs (NBCTG=%d)\n",Prog_Name,NBCONTIG);
fprintf(stderr,"%s: INDEX SCAF OFFSET LENGTH\n",Prog_Name);
for (i = 0; i < NBCONTIG; i++)
fprintf(stderr,"%s: %6d %6d %10lld %10lld\n",Prog_Name,i,
BCONTIG[i].scaf,BCONTIG[i].sbeg,BCONTIG[i].clen);
fprintf(stderr,"%s: List of scaffolds (NBSCAFF=%d)\n",Prog_Name,NBSCAFF);
for (i = 0; i < NBSCAFF; i++)
fprintf(stderr,"%s: %6d %s\n",Prog_Name,i,Get_Hash_String(BHASH,i));
}
}
#endif
free(alens);
free(blens);
}
/*******************************************************************************************
*
* Chenxi's plotting code
*
*******************************************************************************************/
static int USORT(const void *l, const void *r)
{ uint64 x = *((uint64 *) l);
uint64 y = *((uint64 *) r);
if (x > y)
return (1);
return (-1);
}
/* Currently not needed
static void axisReverse(uint64 *sarray, int64 *caxis, int64 soff, int beg, int end,
int *cbeg, int *cend)
{ int i, c, clen;
int64 coff;
coff = caxis[(uint32) sarray[beg]];
for (i = beg; i < end; i++)
{ c = (uint32) sarray[i];
soff -= caxis[c] - coff; // gap
clen = cend[c] - cbeg[c];
soff -= clen; // ctg
coff = caxis[c] + clen;
caxis[c] = soff;
}
}
*/
// Now string length of a name is capped by MAX_LAB_LEN
// If the length N exceeds the limit then
// substring name[MAX_LAB_LEN-2,N-2] is replaced by a "*"
static void addSeqName(char *names, uint32 n, uint32 m, int c0, int c1,
uint32 s, Hash_Table *hash, GDB *gdb, Contig_Range *chord, int rank,
char **_names, uint32 *_n, uint32 *_m)
{ uint32 l, n0;
int64 p;
char *name;
n0 = n;
if (PRINTSID)
{ l = Number_Digits(s+1);
expandBuffer(&names, &n, &m, l+1);
sprintf(names+n,"%u",s+1);
n += l;
}
else
{ name = Get_Hash_String(hash,s);
l = strlen(name);
expandBuffer(&names, &n, &m, l+1);
sprintf(names+n,"%s",name);
n += l;
}
if (chord[c0].beg > 0 ||
gdb->scaffolds[s].fctg != c0 || // start from first
gdb->scaffolds[s].ectg != c1+1 ||
chord[c1].end != gdb->contigs[c1].clen) // end at last
{ // partial scaffold
p = gdb->contigs[c0].sbeg + chord[c0].beg;
p += 1; // make it 1-based
l = Number_Digits(p);
l += 1;
expandBuffer(&names, &n, &m, l+1);
sprintf(names+n,"_%lld",p);
n += l;
p = gdb->contigs[c1].sbeg + chord[c1].end;
l = Number_Digits(p);
l += 1;
expandBuffer(&names, &n, &m, l+1);
sprintf(names+n,"-%lld",p);
n += l;
}
if (rank < 0)
{ // add a prime
expandBuffer(&names, &n, &m, 2);
names[n++] = '\'';
names[n] = '\0';
}
if (n > n0 + MAX_LAB_LEN) {
// string length exceed limits
l = n - n0;
if (rank < 0) {
names[n0+MAX_LAB_LEN-3] = '*';
names[n0+MAX_LAB_LEN-2] = names[n-2]; // the last character
names[n0+MAX_LAB_LEN-1] = names[n-1]; // the prime
names[n0+MAX_LAB_LEN] = '\0';
} else {
names[n0+MAX_LAB_LEN-2] = '*';
names[n0+MAX_LAB_LEN-1] = names[n-1]; // the last character
names[n0+MAX_LAB_LEN] = '\0';
}
n = n0 + MAX_LAB_LEN;
}
n++; // the null terminator
// assign_vars:
*_names = names;
*_n = n;
*_m = m;
}
static double seqNameWidth(char *names, int n)
{ int i, c;
double l, w;
w = 0;
for (i = 0; i < n; i++)
{ l = 0;
while (*names != '\0')
{ c = (uint8) (*names);
if (c < 33 || c > 126)
{ fprintf(stderr,"%s: unsupported character '%c'\n",Prog_Name,*names);
exit (1);
}
l += HELVETICA[c];
names++;
}
if (l > w) w = l;
names++;
}
return (w);
}
static double seqNameRenderWidth(char *names, int n, int64 *soff, double unit, double space)
{ int i, c;
double l, w, s;
w = 0;
for (i = 0; i < n; i++)
{ s = (i == 0 ? soff[0] : soff[i] - soff[i-1]);
if (s * unit < space)
{ names += strlen(names) + 1;
continue;
}
l = 0;
while (*names != '\0')
{ c = (uint8) (*names);
if (c < 33 || c > 126)
{ fprintf(stderr,"%s: unsupported character '%c'\n",Prog_Name,*names);
exit (1);
}
l += HELVETICA[c];
names++;
}
if (l > w) w = l;
names++;
}
return (w);
}
static double chooseFontSizeByHeight(int64 *soff, int n, double unit, double minf, double maxf)
{ int i;
double s, f;
f = maxf;
for (i = 0; i < n; i++)
{ s = (i == 0 ? soff[0] : soff[i] - soff[i-1]);
s *= unit;
if (s >= minf && s < f) f = s;
}
return (f);
}
int axisConfig(Hash_Table *hash, GDB *gdb, Contig_Range *chord,
int64 **_caxis, int64 **_saxis, char **_names, int64 *_tseq)
{ int i, j, s, r1, r2, mseq, nseq;
uint32 c0, c1, c2, nstr, mstr;
uint64 *sarray;
int64 *caxis, *saxis, tseq;
char *names;
mseq = 0;
for (i = 0; i < gdb->ncontig; i++)
if (chord[i].order >= 0)
mseq++;
sarray = (uint64 *) Malloc(sizeof(uint64)*mseq,"Allocating seq array");
saxis = (int64 *) Malloc(sizeof(int64)*mseq,"Allocating offset array");
caxis = (int64 *) Malloc(sizeof(int64)*gdb->ncontig,"Allocating offset array");
if (LABELS)
{ mstr = 2048;
names = (char *) Malloc(sizeof(char)*mstr,"Allocating name array");
}
else
names = NULL;
mseq = 0;
for (i = 0; i < gdb->ncontig; i++)
if (chord[i].order)
sarray[mseq++] = (uint64) abs(chord[i].order) << 32 | i;
qsort(sarray, mseq, sizeof(uint64), USORT);
c1 = (uint32) sarray[0];
r1 = chord[c1].order;
tseq = 0;
nseq = 0;
nstr = 0;
for (j = 0, i = 1; i < mseq; i++)
{ caxis[c1] = tseq - chord[c1].beg;
tseq += chord[c1].end - chord[c1].beg;
c2 = (uint32) sarray[i];
r2 = chord[c2].order;
if (chord[c1].end < gdb->contigs[c1].clen || // end-clipping
c1 + 1 < c2 || // contigs skipped
gdb->contigs[c1].scaf != gdb->contigs[c2].scaf || // scaffolds switched
r1 != r2 || // ranks changed
chord[c2].beg > 0) // start-clipping
{ // different rank group or gap
// add new seq [j,i)
c0 = (uint32) sarray[j];
s = gdb->contigs[c0].scaf; // get scaffold id
if (LABELS)
addSeqName(names,nstr,mstr,c0,c1,s,hash,gdb,chord,r1,&names,&nstr,&mstr);
saxis[nseq++] = tseq;
// reverse ctg [j,i)
// if (r1 < 0) axisReverse(sarray, caxis, tseq, j, i, cbeg, cend);
j = i;
}
else
tseq += gdb->contigs[c2].sbeg - gdb->contigs[c1].sbeg - gdb->contigs[c1].clen;
c1 = c2;
r1 = r2;
}
// add new seq [j,i)
caxis[c1] = tseq - chord[c1].beg;
tseq += chord[c1].end - chord[c1].beg;
c0 = (uint32) sarray[j];