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pbwtIO.c
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pbwtIO.c
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/* File: pbwtIO.c
* Author: Richard Durbin ([email protected])
* Copyright (C) Genome Research Limited, 2013-
*-------------------------------------------------------------------
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* http://www.apache.org/licenses/LICENSE-2.0
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*-------------------------------------------------------------------
* Description: read/write functions for pbwt package
* Exported functions:
* HISTORY:
* Last edited: Mar 11 16:38 2016 (rd)
* readPhase updated for chromopainter and chromopainter v2 formats
* Created: Thu Apr 4 11:42:08 2013 (rd)
*-------------------------------------------------------------------
*/
#include "pbwt.h"
#include <ctype.h>
int nCheckPoint = 0 ; /* if set non-zero write pbwt and sites files every n sites when parsing external files */
static BOOL isWriteImputeRef = FALSE ; /* modifies WriteSites() and WriteHaplotypes() for pbwtWriteImputeRef */
/* basic function to store packed PBWT */
void pbwtWrite (PBWT *p, FILE *fp) /* just writes compressed pbwt in yz */
{
if (!p || !p->yz) die ("pbwtWrite called without a valid pbwt") ;
if (!p->aFstart || !p->aFend) die ("pbwtWrite called without start and end indexes") ;
/* version 2 added start and end indexes */
if (fwrite ("PBW3", 1, 4, fp) != 4) /* version 3 with 8 byte pbwt size */
die ("error writing PBWT in pbwtWrite") ;
if (fwrite (&p->M, sizeof(int), 1, fp) != 1)
die ("error writing M in pbwtWrite") ;
if (fwrite (&p->N, sizeof(int), 1, fp) != 1)
die ("error writing N in pbwtWrite") ;
if (fwrite (p->aFstart, sizeof(int), p->M, fp) != p->M)
die ("error writing aFstart in pbwtWrite") ;
if (fwrite (p->aFend, sizeof(int), p->M, fp) != p->M)
die ("error writing aFend in pbwtWrite") ;
long n = arrayMax(p->yz) ;
if (fwrite (&n, sizeof(long), 1, fp) != 1)
die ("error writing n in pbwtWrite") ;
if (fwrite (" ", 1, 4, fp) != 4)
die ("error writing padding space in pbwtWrite") ;
if (fwrite (arrp(p->yz, 0, uchar), sizeof(uchar), arrayMax(p->yz), fp) != arrayMax(p->yz))
die ("error writing data in pbwtWrite") ;
fprintf (logFile, "written %ld chars pbwt: M, N are %d, %d\n", arrayMax(p->yz), p->M, p->N) ;
}
void pbwtWriteSites (PBWT *p, FILE *fp)
{
if (!p || !p->sites) die ("pbwtWriteSites called without sites") ;
int i ;
for (i = 0 ; i < p->N ; ++i)
{ Site *s = arrp(p->sites, i, Site) ;
if (isWriteImputeRef)
fprintf (fp, "site%d\t%d", i+1, s->x) ;
else
fprintf (fp, "%s\t%d", p->chrom ? p->chrom : ".", s->x) ;
fprintf (fp, "\t%s", dictName (variationDict, s->varD)) ;
fputc ('\n', fp) ;
}
if (ferror (fp)) die ("error writing sites file") ;
fprintf (logFile, "written %d sites from %d to %d\n", p->N,
arrp(p->sites, 0, Site)->x, arrp(p->sites, p->N-1, Site)->x) ;
}
void pbwtWriteSamples (PBWT *p, FILE *fp)
{
if (!p || !p->samples) die ("pbwtWriteSamples called without samples") ;
static const char *typeStr = "\0ifZ" ;
int i, j, count = 0 ;
for (i = 0 ; i < p->M ; i += pbwtSamplePloidy (p, i), count++)
{ Sample *s = sample (arr(p->samples, i, int)) ;
writeMetaData(sampleName(s), s->metaData, fp) ;
}
if (ferror (fp)) die ("error writing samples file") ;
fprintf (logFile, "written %d samples\n", count) ;
}
void writeDataOffset (FILE *fp, char *name, Array data, Array offset, int N)
{
if (!offset || !data) die ("write %s called without data", name) ;
int dummy = -1 ; /* ugly hack to mark that we now use longs not ints */
if (fwrite (&dummy, sizeof(int), 1, fp) != 1)
die ("error writing marker in write %s", name) ;
long n = arrayMax(data) ;
if (fwrite (&n, sizeof(long), 1, fp) != 1)
die ("error writing n in write %s", name) ;
if (fwrite (arrp(data, 0, uchar), sizeof(uchar), n, fp) != n)
die ("error writing data in write %s", name) ;
if (fwrite (arrp(offset, 0, long), sizeof(long), N, fp) != N)
die ("error writing offsets in write %s", name) ;
fprintf (logFile, "written %ld chars compressed %s data\n", n, name) ;
}
void pbwtWriteMissing (PBWT *p, FILE *fp)
{ writeDataOffset (fp, "missing", p->zMissing, p->missingOffset, p->N) ; }
void pbwtWriteDosage (PBWT *p, FILE *fp)
{ writeDataOffset (fp, "dosage", p->zDosage, p->dosageOffset, p->N) ; }
void pbwtWriteReverse (PBWT *p, FILE *fp)
{
if (!p || !p->zz) die ("pbwtWriteReverse called without reverse pbwt") ;
Array tz = p->yz ; p->yz = p->zz ;
int* tstart = p->aFstart ; p->aFstart = p->aRstart ;
int* tend = p->aFend ; p->aFend = p->aRend ;
fprintf (logFile, "reverse: ") ; pbwtWrite (p, fp) ;
p->yz = tz ; p->aFstart = tstart ; p->aFend = tend ;
}
void pbwtWriteAll (PBWT *p, char *root)
{
FILE *fp ;
#define FOPEN_W(tag) if (!(fp = fopenTag (root, tag, "w"))) die ("failed to open root.%s", tag)
FOPEN_W("pbwt") ; pbwtWrite (p, fp) ; fclose (fp) ;
if (p->sites) { FOPEN_W("sites") ; pbwtWriteSites (p, fp) ; fclose (fp) ; }
if (p->samples) { FOPEN_W("samples") ; pbwtWriteSamples (p, fp) ; fclose (fp) ; }
if (p->missingOffset) { FOPEN_W("missing") ; pbwtWriteMissing (p, fp) ; fclose (fp) ; }
if (p->dosageOffset) { FOPEN_W("dosage") ; pbwtWriteDosage (p, fp) ; fclose (fp) ; }
if (p->zz) { FOPEN_W("reverse") ; pbwtWriteReverse (p, fp) ; fclose (fp) ; }
}
void pbwtWritePhase (PBWT *p, char *filename)
{
FILE *fp ;
if (!(fp = fopen (filename, "w"))) die ("failed to open %s",filename);
fprintf(fp,"%i\n",p->M);
fprintf(fp,"%i\nP",p->N);
int i ; for (i = 0 ; i < p->N ; i++) fprintf(fp," %i",arrayp(p->sites,i,Site)->x);
fprintf(fp,"\n");
pbwtWriteTransposedHaplotypes(p,fp);
}
void pbwtCheckPoint (PbwtCursor *u, PBWT *p)
{
static BOOL isA = TRUE ;
char fileNameRoot[20] ;
pbwtCursorToAFend (u, p) ;
sprintf (fileNameRoot, "check_%c", isA ? 'A' : 'B') ;
pbwtWriteAll (p, fileNameRoot) ;
isA = !isA ;
}
/*******************************/
PBWT *pbwtRead (FILE *fp)
{
int m, n ;
long nz ;
PBWT *p ;
static char tag[5] = "test" ;
char pad[4] ;
int version ;
if (fread (tag, 1, 4, fp) != 4) die ("failed to read 4 char tag - is file readable?") ;
if (!strcmp (tag, "PBW3")) version = 3 ; /* current version */
else if (!strcmp (tag, "PBW2")) version = 2 ; /* with 4 byte count */
else if (!strcmp (tag, "PBWT")) version = 1 ; /* without start, end indexes */
else if (!strcmp (tag, "GBWT")) version = 0 ; /* earliest version */
else die ("failed to recognise file type %s in pbwtRead - was it written by pbwt?", tag) ;
if (fread (&m, sizeof(int), 1, fp) != 1) die ("error reading m in pbwtRead") ;
if (fread (&n, sizeof(int), 1, fp) != 1) die ("error reading n in pbwtRead") ;
p = pbwtCreate (m, n) ;
free(p->aFstart);
if (version > 1) /* read aFstart and aFend */
{ p->aFstart = myalloc (m, int) ;
if (fread (p->aFstart, sizeof(int), m, fp) != m) die ("error reading aFstart in pbwtRead") ;
p->aFend = myalloc (m, int) ;
if (fread (p->aFend, sizeof(int), m, fp) != m) die ("error reading aFend in pbwtRead") ;
}
else /* set aFstart to 0..M-1, leave aFend empty */
{ p->aFstart = myalloc (m, int) ;
int i ; for (i = 0 ; i < m ; ++i) p->aFstart[i] = i ;
}
if (version <= 2)
{ if (fread (&n, sizeof(int), 1, fp) != 1) die ("error reading pbwt file") ;
nz = n ;
}
else
if (fread (&nz, sizeof(long), 1, fp) != 1 ||
fread (pad, 1, 4, fp) != 4) die ("error reading pbwt file") ;
p->yz = arrayCreate (nz, uchar) ;
array(p->yz, nz-1, uchar) = 0 ; /* sets arrayMax */
if (fread (arrp(p->yz, 0, uchar), sizeof(uchar), nz, fp) != nz)
die ("error reading data in pbwt file") ;
fprintf (logFile, "read pbwt %s file with %ld bytes: M, N are %d, %d\n", tag, nz, p->M, p->N) ;
return p ;
}
static BOOL readMatchChrom (char **pChrom, FILE *fp)
{
char *newChrom = fgetword (fp) ;
if (strcmp (newChrom, "."))
{ if (!*pChrom)
*pChrom = strdup (newChrom) ;
else if (strcmp (newChrom, *pChrom))
return FALSE ;
}
return TRUE ;
}
Array pbwtReadSitesFile (FILE *fp, char **chrom)
{
char c ;
Site *s ;
int line = 1 ;
Array varTextArray = arrayCreate (256, char) ;
Array sites = arrayCreate (4096, Site) ;
while (!feof(fp))
if (readMatchChrom (chrom, fp)) /* if p->chrom then match, else set if not "." */
{ if (feof(fp)) break ;
s = arrayp(sites, arrayMax(sites), Site) ;
s->x = 0 ; while (isdigit(c = fgetc(fp))) s->x = s->x*10 + (c-'0') ;
if (!feof(fp) && c != '\n')
{ if (!isspace (c)) die ("bad position line %d in sites file", line) ;
while (isspace(c = fgetc(fp)) && c != '\n') ;
if (c == '\n') die ("bad end of line at line %d in sites file", line) ;
int i = 0 ; array(varTextArray, i++, char) = c ;
while ((c = fgetc(fp)) && c != '\n')
array(varTextArray, i++, char) = c ;
array(varTextArray, i, char) = 0 ;
dictAdd (variationDict, arrayp(varTextArray,0,char), &s->varD) ;
while (c != '\n' && !feof(fp)) c = fgetc(fp) ;
}
++line ;
}
else if (!feof(fp))
die ("failed to match chromosome in sites file: line %d", line) ;
if (ferror (fp)) die ("error reading sites file") ;
fprintf (logFile, "read %ld sites on chromosome %s from file\n", arrayMax(sites), *chrom) ;
arrayDestroy (varTextArray) ;
return sites ;
}
void pbwtReadSites (PBWT *p, FILE *fp)
{
if (!p) die ("pbwtReadSites called without a valid pbwt") ;
p->sites = pbwtReadSitesFile (fp, &p->chrom) ;
if (arrayMax(p->sites) != p->N)
die ("sites file contains %ld sites not %d as in pbwt", arrayMax(p->sites), p->N) ;
}
Array readRefFreq (PBWT *p, FILE *fp)
{
Array a = arrayCreate (p->N, Site) ;
char chrom[256], var[256] ;
int pos ;
double freq ;
while (!feof(fp))
{ if (fscanf (fp, "%s\t%d\t%lf\t", chrom, &pos, &freq) != 3 && !feof (fp))
die ("can't read ref freq file properly") ;
if (strcmp (chrom, p->chrom))
die ("chromosome mismatch in readRefFreq '%s' is not '%s'", chrom, p->chrom) ;
char *cp = var ; while ((*cp = getc(fp)) != '\n' && !feof(fp)) ++cp ; *cp = 0 ;
Site *s = arrayp(a, arrayMax(a), Site) ;
s->x = pos ;
s->refFreq = freq ;
dictAdd (variationDict, var, &s->varD) ;
}
return a ;
}
void pbwtReadRefFreq (PBWT *p, FILE *fp)
{ if (!p || !p->sites) die ("pbwtReadRefFreq called without current site information") ;
Array a = readRefFreq (p, fp) ;
int i = 0, j = 0 ;
Site *ps = arrp(p->sites,i,Site), *as = arrp(a,j,Site) ;
while (i < p->N)
{ while (j < arrayMax(a) &&
(as->x < ps->x || (as->x == ps->x && as->varD < ps->varD))) { ++j ; ++as ; }
if (ps->x == as->x && ps->varD == as->varD) ps->refFreq = as->refFreq ;
++i ; ++ps ;
}
}
// Array pbwtReadSamplesFile (FILE *fp) /* for now assume all samples diploid */
// /* should add code to this to read father and mother and population
// propose to use IMPUTE2 format for this */
// {
// char *name, c ;
// int line = 0 ;
// Array nameArray = arrayCreate (1024, char) ;
// Array samples = arrayCreate (1024, int) ;
// while (!feof(fp))
// { int n = 0 ;
// while ((c = getc(fp)) && !isspace(c) && !feof (fp)) array(nameArray, n++, char) = c ;
// if (feof(fp)) break ;
// if (!n) die ("no name line %ld in samples file", arrayMax(samples)+1) ;
// array(nameArray, n++, char) = 0 ;
// /* next bit of code deals with header lines for IMPUTE2 samples file, so can read that */
// if (!strcmp (arrp(nameArray,0,char), "ID_1") && !arrayMax(samples))
// { while ((c = getc(fp)) && c != '\n' && !feof(fp)) ; /* remove header line */
// while ((c = getc(fp)) && c != '\n' && !feof(fp)) ; /* and next line of zeroes?? */
// continue ;
// }
// array(samples,arrayMax(samples),int) = sampleAdd(arrp(nameArray,0,char), 0, 0, 0, 0, 0)->nameD ;
// /* now remove the rest of the line, for now */
// while (c != '\n' && !feof(fp)) c = getc(fp) ;
// }
// arrayDestroy (nameArray) ;
// fprintf (logFile, "read %ld sample names\n", arrayMax(samples)) ;
// return samples ;
// }
/*
FMF format - tab delimited flat metadata format where first column is the
sample name followed by metadata in the format key:type:value with type
being Z for a string, f for a real number and i for an integer:
sample1 sex:Z:M height:f:1.73 region:Z:WestEurasia foo:i:10
sample2 sex:Z:F height:f:1.64 region:Z:WestEurasia bar:i:20
*/
/*
FAM format - first 6 columns of the PED format (used for binary PED format). space delimited with no header:
1. Family ID
2. Individual ID
3. Paternal ID
4. Maternal ID
5. Sex (1=male; 2=female; other=unknown)
6. Phenotype (-1=missing; 0=missing; 1=unaffected; 2=affected)
*/
/*
HAPS/SAMPLE and GEN/SAMPLE format - space delimited with at least 3 columns with 2 header lines:
1. individual ID 1 (ID_1)
2. individual ID 2 (ID_2)
3. missing data proportion (missing)
4-. ignored, covariates named in the first header line and type defined in the second header line
(0=for first 3 columns; D=discrete covariate (unsigned int); C=continuous covariate (float); P=continuous phenotype (float); B=binary phenotype (0 or 1))
*/
/*
HAPS/LEGEND/SAMPLE format - space delimited with at least 4 columns with 1 header line :
1. individual ID (sample)
2. group ID 1 (population)
3. group ID 2 (group)
4. sex (1=male; 2=female; other=unknown)
5-. ignored
*/
Array pbwtReadSamplesFile (FILE *fp) {
// populate sample fields from FMF sample file
char *line = calloc(1024, sizeof(char)); line[0] = '\0';
char *key = calloc(128, sizeof(char)); key[0] = '\0';
char *value = calloc(128, sizeof(char)); value[0] = '\0';
char *name = calloc(128, sizeof(char)); name[0] = '\0';
char *str;
char type;
Array samples = arrayCreate (1024, int) ;
while (1) {
char *rmme = line;
line = fgets(line, 1024, fp);
if ( !line ) free(rmme);
if(feof(fp)) break;
else if(sscanf(line, "ID_1%s", name)) { // IMPUTE2 file
die("IMPUTE2 style sample files not yet supported - coming soon");
}
else { // FMF file (single column valid)
str = strtok(line, "\t\n"); // test it works with single column
strcpy(name, str);
int v, k = array(samples,arrayMax(samples),int) = sampleAdd(name) ;
Sample *s = sample (k) ;
while(str = strtok(0, "\t\n"))
{
if(sscanf(str, "%127[^:]:%1[^:]:%127[^:]", key, &type, value) == 3)
{
addMetaData(s->metaData, key, value, type) ;
}
if(!strcasecmp(key, "mother")) { mother (s, value) ; }
if(!strcasecmp(key, "father")) { father (s, value) ; }
if(!strcasecmp(key, "family")||!strcasecmp(key, "familyID")) { familyName (s, value) ; }
if(!strcasecmp(key, "pop")||!strcasecmp(key, "population")) { popName (s, value) ; }
if(!strcasecmp(key, "gender")||!strcasecmp(key, "sex"))
{
if(!strcasecmp(value, "M")||!strcasecmp(value, "male")) s->isMale = TRUE ;
if(!strcasecmp(value, "F")||!strcasecmp(value, "female")) s->isFemale = TRUE ;
}
}
}
}
free(line); free(key); free(value); free(name);
fprintf (logFile, "read %ld sample names\n", arrayMax(samples)) ;
return samples ;
}
void pbwtReadSamples (PBWT *p, FILE *fp)
{
if (!p) die ("pbwtReadSamples called without a valid pbwt") ;
Array samples = pbwtReadSamplesFile (fp) ;
int i,j, count_x2 = 0, count_x1 = 0, count_y1 = 0, count_y0 = 0, count2 = 0;
p->samples = arrayReCreate(p->samples, p->M, int) ;
for (i=0; i<arrayMax(samples); i++)
{
int k = arr(p->samples, i, int);
Sample *s = sample (k) ;
if ( s->isFemale ) { count_x2++; count_y0++; count2++; }
else { count_x1++; count_y1++; count2++; }
}
if ( 2*count2 == p->M )
fprintf (logFile, "Note: number of haplotypes (%ld) is consistent with %d diploid samples\n", arrayMax(samples), p->M) ;
else if ( 2*count_x2 + count_x1 == p->M )
{
p->isX = TRUE;
fprintf (logFile, "Note: number of haplotypes (%d) is consistent with %d haploid and %d diploid samples\n", p->M, count_x1,count_x2) ;
}
else if ( count_y1 == p->M )
{
p->isY = TRUE;
fprintf (logFile, "Note: number of haplotypes (%d) consistent with %d haploid samples and %d samples with zero ploidy\n", p->M, count_y1,count_y0) ;
}
else
die ("number of haplotypes (%d) is not consistent with the number of samples (%ld): expected %d, %d or %d haplotypes", p->M, arrayMax(samples),count2,2*count_x2 + count_x1,count_y1) ;
for (i=0,j=0; i<arrayMax(samples); i++)
{
int k = arr(samples, i, int);
Sample *s = sample (k) ;
if (p->isY && s->isFemale) continue ;
array(p->samples, j++, int) = k ;
if (p->isX && s->isMale) continue ;
array(p->samples, j++, int) = k ;
}
arrayDestroy (samples) ;
}
static void readDataOffset (FILE *fp, char *name, Array *data, Array *offset, int N)
{
long n ; /* size of data file */
int dummy ;
if (fread (&dummy, sizeof(int), 1, fp) != 1)
die ("read error in read %s", name) ;
if (dummy != -1) n = dummy ; /* old version with ints not longs */
else if (fread (&n, sizeof(long), 1, fp) != 1)
die ("read error in read %s", name) ;
*data = arrayReCreate (*data, n, uchar) ;
if (fread (arrp(*data, 0, uchar), sizeof(uchar), n, fp) != n)
die ("error reading z%s in pbwtRead%s", name, name) ;
arrayMax(*data) = n ;
fprintf (logFile, "read %ld chars compressed %s data\n", n, name) ;
*offset = arrayReCreate (*offset, N, long) ;
if (dummy != -1) /* old version with ints not longs */
{ /* abuse *offset to hold ints, then update in place */
if (fread (arrp(*offset, 0, int), sizeof(int), N, fp) != N)
die ("error reading %s in pbwtRead%s", name, name) ;
for (n = N ; n-- ;)
arr(*offset, n, long) = arr(*offset, n, int) ; /* !! */
}
else
if (fread (arrp(*offset, 0, long), sizeof(long), N, fp) != N)
die ("error reading %s in pbwtRead%s", name, name) ;
arrayMax(*offset) = N ;
}
void pbwtReadMissing (PBWT *p, FILE *fp)
{ readDataOffset (fp, "missing", &p->zMissing, &p->missingOffset, p->N) ; }
void pbwtReadDosage (PBWT *p, FILE *fp)
{ readDataOffset (fp, "dosage", &p->zDosage, &p->dosageOffset, p->N) ; }
void pbwtReadReverse (PBWT *p, FILE *fp)
{
if (!p) die ("pbwtReadReverse called without a valid pbwt") ;
PBWT *q = pbwtRead (fp) ;
if (q->M != p->M || q->N != p->N)
die ("M %d or N %d in reverse don't match %, %d in forward", q->M, q->N, p->M, p->N) ;
p->zz = q->yz ; q->yz = 0 ;
p->aRstart = q->aFstart ; q->aFstart = 0 ;
p->aRend = q->aFend ; q->aFend = 0 ;
pbwtDestroy (q) ;
}
PBWT *pbwtReadAll (char *root)
{
PBWT *p ;
FILE *fp ;
if ((fp = fopenTag (root, "pbwt", "r"))) { p = pbwtRead (fp) ; fclose (fp) ; }
else die ("failed to open %s.pbwt", root) ;
if ((fp = fopenTag (root, "sites","r"))) { pbwtReadSites (p, fp) ; fclose (fp) ; }
if ((fp = fopenTag (root, "samples","r"))) { pbwtReadSamples (p, fp) ; fclose (fp) ; }
if ((fp = fopenTag (root, "missing","r"))) { pbwtReadMissing (p, fp) ; fclose (fp) ; }
if ((fp = fopenTag (root, "dosage","r"))) { pbwtReadDosage (p, fp) ; fclose (fp) ; }
if ((fp = fopenTag (root, "reverse","r"))) { pbwtReadReverse (p, fp) ; fclose (fp) ; }
return p ;
}
/****************** MaCS file parsing *****************/
static void parseMacsHeader (FILE *fp, int *M, double *L) /* parse MACS file header */
{
if (strcmp (fgetword (fp), "COMMAND:")) die ("MaCS COMMAND line not found") ;
fgetword (fp) ; /* the command */
*M = atoi(fgetword(fp)) ; if (!*M) die ("failed to get M") ;
*L = atof(fgetword(fp)) ; if (!*L) die ("failed to get L") ;
while (fgetc(fp) != '\n') ; /* ignore rest of line */
if (strcmp (fgetword (fp), "SEED:")) die ("SEED line not found") ;
while (fgetc(fp) != '\n') ; /* ignore rest of line */
}
static BOOL parseMacsSite (FILE *fp, Site *s, int M, double L, uchar *yp) /* parse MACS site line */
{
static uchar conv[256] ;
static BOOL isFirst = TRUE ;
int number ;
if (isFirst) { conv['0'] = 0 ; conv['1'] = 1 ; isFirst = FALSE ; }
if (feof (fp)) return FALSE ;
if (strcmp (fgetword (fp), "SITE:")) return FALSE;
number = atoi(fgetword(fp)) ; /* this is the site number */
s->x = (int) (L * atof(fgetword(fp))) ;
double dummy = atof(fgetword(fp)) ; /* ignore the time - dummy stops compile warning */
while (M--)
*yp++ = conv[getc(fp)] ;
if (feof (fp)) return FALSE ;
if (getc(fp) != '\n') die ("end of line error for MaCS SITE %d", number) ;
return TRUE ;
}
PBWT *pbwtReadMacs (FILE *fp)
{
PBWT *p ;
int M ;
double L ;
int i,j, nxPack, nyPack, nUnpack, n0 ;
int nxTot = 0, nyTot = 0 ;
uchar *x ;
int *a ;
PbwtCursor *u ;
parseMacsHeader (fp, &M, &L) ;
p = pbwtCreate (M, 0) ;
p->sites = arrayCreate(4096, Site) ;
u = pbwtCursorCreate (p, TRUE, TRUE) ;
x = myalloc (M+1, uchar) ; x[M] = Y_SENTINEL ; /* sentinel required for packing */
while (parseMacsSite (fp, arrayp(p->sites,p->N,Site), M, L, x))
{ for (j = 0 ; j < M ; ++j) u->y[j] = x[u->a[j]] ; /* next character in sort order: BWT */
pbwtCursorWriteForwards (u) ;
p->N++ ;
if (nCheckPoint && !(p->N % nCheckPoint)) pbwtCheckPoint (u, p) ;
}
pbwtCursorToAFend (u, p) ;
fprintf (logFile, "read MaCS file: M, N are\t%d\t%d\n", M, p->N) ;
if (isStats)
fprintf (logFile, " xtot, ytot are\t%d\t%d\n", nxTot, nyTot) ;
free(x) ; pbwtCursorDestroy (u) ;
return p ;
}
/************* read vcfq files, made with vcf query ... ***************/
static char* getVariation (FILE *fp)
{
static Array a = 0 ;
char c ;
int i = 0 ;
if (!a) a = arrayCreate (64, char) ;
while (!isspace(c = getc(fp)) && !feof(fp)) array(a,i++,char) = c ;
array(a,i++,char) = c ;
while (!isspace(c = getc(fp)) && !feof(fp)) array(a,i++,char) = c ;
array(a,i++,char) = 0 ;
return arrp(a,0,char) ;
}
static BOOL parseVcfqLine (PBWT **pp, FILE *fp, Array x)
{
char c, *chrom, *var ;
int pos, m, len ;
Site *s ;
PBWT *p = *pp ;
if (!p) /* first call on a file - don't know M yet */
chrom = strdup (fgetword (fp)) ;
else
while (!feof (fp) && !readMatchChrom (&p->chrom, fp))
while (!feof (fp) && (getc (fp) != '\n')) ; /* ignore rest of line */
if (feof (fp)) return 0 ;
pos = atoi (fgetword (fp)) ;
var = getVariation (fp) ;
m = 0 ;
while ((c = getc (fp)))
switch (c)
{ case EOF: return 0 ;
case '\n': goto endOfLine ; /* -1 is EOF */
case '0': array(x,m++,uchar) = 0 ; break ;
case '1': array(x,m++,uchar) = 1 ; break ;
case '|': case '/': case '\\': case '\t': break ; /* could check ploidy here */
default: die ("unexpected character %d in vcfq file genotype section") ;
}
endOfLine:
if (feof (fp)) return FALSE ;
if (p && m != p->M) die ("length mismatch reading vcfq line") ;
if (!*pp)
{ p = *pp = pbwtCreate (m, 0) ;
if (strcmp (chrom, ".")) p->chrom = chrom ;
p->sites = arrayCreate(4096, Site) ;
array(x,p->M,uchar) = Y_SENTINEL ; /* sentinel required for packing */
}
s = arrayp(p->sites, arrayMax(p->sites), Site) ;
s->x = pos ;
dictAdd (variationDict, var, &s->varD) ;
++p->N ;
return TRUE ;
}
typedef BOOL (*ParseLineFunc)(PBWT** pp, FILE *f, Array a) ;
static PBWT *pbwtReadLineFile (FILE *fp, char* type, ParseLineFunc parseLine)
{
PBWT *p = 0 ;
int j ;
uchar *x ; /* original, sorted, compressed */
int *a ;
Array xArray = arrayCreate (10000, uchar) ;
PbwtCursor *u ;
while ((*parseLine) (&p, fp, xArray)) /* create p first time round */
{ if (!p->yz) /* first line; p was just made! */
{ p->yz = arrayCreate(4096*32, uchar) ;
u = pbwtCursorCreate (p, TRUE, TRUE) ;
}
x = arrp(xArray,0,uchar) ;
for (j = 0 ; j < p->M ; ++j) u->y[j] = x[u->a[j]] ;
pbwtCursorWriteForwards (u) ;
if (nCheckPoint && !(p->N % nCheckPoint)) pbwtCheckPoint (u, p) ;
}
pbwtCursorToAFend (u, p) ;
fprintf (logFile, "read %s file", type) ;
if (p->chrom) fprintf (logFile, " for chromosome %s", p->chrom) ;
fprintf (logFile, ": M, N are\t%d\t%d; yz length is %ld\n", p->M, p->N, arrayMax(p->yz)) ;
arrayDestroy(xArray) ; pbwtCursorDestroy (u) ;
return p ;
}
typedef BOOL (*ParseTwoLineFunc)(PBWT** pp, FILE *f, FILE *l, Array a) ;
static PBWT *pbwtReadLineTwoFile (FILE *fp, FILE *lp, char* type, ParseTwoLineFunc parseLine)
{
PBWT *p = 0 ;
int j ;
uchar *x ; /* original, sorted, compressed */
int *a ;
Array xArray = arrayCreate (10000, uchar) ;
PbwtCursor *u ;
/* skip header of legend file */
while (!feof(lp))
{ char c = getc(lp) ; if (c == '\n') break ;
}
while ((*parseLine) (&p, fp, lp, xArray)) /* create p first time round */
{ if (!p->yz) /* first line; p was just made! */
{ p->yz = arrayCreate(4096*32, uchar) ;
u = pbwtCursorCreate (p, TRUE, TRUE) ;
}
x = arrp(xArray,0,uchar) ;
for (j = 0 ; j < p->M ; ++j) u->y[j] = x[u->a[j]] ;
pbwtCursorWriteForwards (u) ;
if (nCheckPoint && !(p->N % nCheckPoint)) pbwtCheckPoint (u, p) ;
}
pbwtCursorToAFend (u, p) ;
fprintf (stderr, "read %s file", type) ;
if (p->chrom) fprintf (stderr, " for chromosome %s", p->chrom) ;
fprintf (stderr, ": M, N are\t%d\t%d; yz length is %ld\n", p->M, p->N, arrayMax(p->yz)) ;
arrayDestroy(xArray) ; pbwtCursorDestroy (u) ;
return p ;
}
PBWT *pbwtReadVcfq (FILE *fp) { return pbwtReadLineFile (fp, "vcfq", parseVcfqLine) ; }
/*************** read impute2 .gen format - contains sites not samples **********/
static long int nGenMissing ;
static BOOL parseGenLine (PBWT **pp, FILE *fp, Array x) /* based on parseVcfqLine() */
{
PBWT *p = *pp ;
fgetword(fp) ; fgetword(fp) ; /* ignore first two name fields */
int pos = atoi (fgetword (fp)) ;
char *var = getVariation (fp) ; /* but need to change ' ' separator to '\t' */
if (feof (fp)) return FALSE ;
char *cp = var ; while (*cp && *cp != ' ') ++cp ; if (*cp == ' ') *cp = '\t' ; else die ("missing separator in line %d, var is %d", p?p->N:0, var) ;
int m = 0, nscan ;
while (!feof(fp))
{ char c = getc(fp) ; if (c == '\n') break ; else if (!isspace(c)) ungetc (c, fp) ;
float f0, f1, f2 ;
if ((nscan = fscanf (fp, "%f %f %f", &f0, &f1, &f2) != 3))
die ("bad line %d, %d floats found, m %d, pos %d, var %s", p ? p->N : 0, nscan, m, pos, var) ;
if (f0 + f1 + f2 == 0) /* missing genotype */
{ f0 = 1 ; ++nGenMissing ; }
if (f0 + f1 + f2 < 0.98)
die ("inconsistent genotype in gen file: %f %f %f at %d line %d",
f0, f1, f2, m, p ? p->N : 0) ;
if (f0 > f1 && f0 > f2) { array(x,m++,uchar) = 0 ; array(x,m++,uchar) = 0 ; }
else if (f1 > f2) { array(x,m++,uchar) = 0 ; array(x,m++,uchar) = 1 ; }
else /* f2 is largest */ { array(x,m++,uchar) = 1 ; array(x,m++,uchar) = 1 ; }
}
if (feof (fp)) return FALSE ;
if (p && m != p->M) die ("length mismatch reading vcfq line") ;
if (!*pp)
{ p = *pp = pbwtCreate (m, 0) ;
p->sites = arrayCreate(4096, Site) ;
array(x,p->M,uchar) = Y_SENTINEL ; /* sentinel required for packing */
}
Site *s = arrayp(p->sites, arrayMax(p->sites), Site) ;
s->x = pos ;
dictAdd (variationDict, var, &s->varD) ;
++p->N ;
return TRUE ;
}
static BOOL parseHapLine (PBWT **pp, FILE *fp, Array x) /* same as parseGenLine - slightly simpler */
{
PBWT *p = *pp ;
fgetword(fp) ; fgetword(fp) ; /* ignore first two name fields */
int pos = atoi (fgetword (fp)) ;
char *var = getVariation (fp) ; /* but need to change ' ' separator to '\t' */
if (feof (fp)) return FALSE ;
char *cp = var ; while (*cp && *cp != ' ') ++cp ; if (*cp == ' ') *cp = '\t' ; else die ("missing separator in line %d, var is %d", p?p->N:0, var) ;
int m = 0, nscan ;
while (!feof(fp))
{ char c = getc(fp) ; if (c == '\n') break ; else if (!isspace(c)) ungetc (c, fp) ;
float f0, f1 ;
if ((nscan = fscanf (fp, "%f %f", &f0, &f1) != 2))
{ warn ("bad line %d, %d floats found, m %d, pos %d, var %s - aborting", p ? p->N : 0, nscan, m, pos, var) ;
return FALSE ;
}
array(x,m++,uchar) = f0 ; array(x,m++,uchar) = f1 ; /* haps are phased, put straight in as is */
}
if (feof (fp)) return FALSE ;
if (p && m != p->M) die ("length mismatch reading haps line") ;
if (!*pp)
{ p = *pp = pbwtCreate (m, 0) ;
p->sites = arrayCreate(4096, Site) ;
array(x,p->M,uchar) = Y_SENTINEL ; /* sentinel required for packing */
}
Site *s = arrayp(p->sites, arrayMax(p->sites), Site) ;
s->x = pos ;
dictAdd (variationDict, var, &s->varD) ;
++p->N ;
return TRUE ;
}
static BOOL parseHapLegendLine (PBWT **pp, FILE *fp, FILE *lp, Array x) /* same as parseGenLine - slightly simpler */
{
PBWT *p = *pp ;
fgetword(lp) ; /* ignore first name field */
int pos = atoi (fgetword (lp)) ;
char *var = getVariation (lp) ; /* but need to change ' ' separator to '\t' */
if (feof (lp)) return FALSE ;
char *cp = var ; while (*cp && *cp != ' ') ++cp ; if (*cp == ' ') *cp = '\t' ; else die ("missing separator in line %d, var is %d", p?p->N:0, var) ;
while (!feof(lp))
{ char c = getc(lp) ; if (c == '\n') break ;
}
int m = 0, nscan ;
while (!feof(fp))
{ char c = getc(fp) ; if (c == '\n') break ; else if (!isspace(c)) ungetc (c, fp) ;
float f0, f1 ;
if ((nscan = fscanf (fp, "%f %f", &f0, &f1) != 2))
{ warn ("bad line %d, %d floats found, m %d, pos %d, var %s - aborting", p ? p->N : 0, nscan, m, pos, var) ;
return FALSE ;
}
array(x,m++,uchar) = f0 ; array(x,m++,uchar) = f1 ; /* haps are phased, put straight in as is */
}
if (feof (fp)) return FALSE ;
if (p && m != p->M) die ("length mismatch reading haps line") ;
if (!*pp)
{ p = *pp = pbwtCreate (m, 0) ;
p->sites = arrayCreate(4096, Site) ;
array(x,p->M,uchar) = Y_SENTINEL ; /* sentinel required for packing */
}
Site *s = arrayp(p->sites, arrayMax(p->sites), Site) ;
s->x = pos ;
dictAdd (variationDict, var, &s->varD) ;
++p->N ;
return TRUE ;
}
PBWT *pbwtReadGen (FILE *fp, char *chrom)
{
nGenMissing = 0 ;
PBWT *p = pbwtReadLineFile (fp, "gen", parseGenLine) ;
p->chrom = strdup (chrom) ;
if (nGenMissing) fprintf (logFile, "%ld missing genotypes set to 00\n", nGenMissing) ;
return p ;
}
PBWT *pbwtReadHap (FILE *fp, char *chrom)
{
PBWT *p = pbwtReadLineFile (fp, "hap", parseHapLine) ;
p->chrom = strdup (chrom) ;
return p ;
}
PBWT *pbwtReadHapLegend (FILE *fp, FILE *lp, char *chrom)
{
PBWT *p = pbwtReadLineTwoFile (fp, lp, "hap-legend", parseHapLegendLine) ;
p->chrom = strdup (chrom) ;
return p ;
}
PBWT *pbwtReadPhase (FILE *fp) /* Li and Stephens PHASE format */
{
int nhaps=0,nsnps=0,ninds=0;
int version=2;
int l1=atoi(fgetword (fp)) ; if (getc(fp) != '\n') die ("bad first line in phase file") ;
int l2 = atoi (fgetword (fp)) ; if (getc(fp) != '\n') die ("bad second line in phase file") ;
char * tc=fgetword (fp);
int l3 = atoi (tc) ;
if (tc[0] == 'P') { // version 2
nhaps=l1;
nsnps=l2;
ninds=nhaps/2;
}else{ // version 1
if (getc(fp) != '\n') die ("bad third line in phase file") ;
ninds=l2;
nhaps=l2*2;
nsnps=l3;
fgetword (fp); /* Remove the initial P */
version=1;
}
fprintf(logFile,"Reading %i SNPs %i haplotypes and %i individuals from PHASE format version %i\n",nsnps,nhaps,ninds,version);
PBWT *p = pbwtCreate (nhaps, nsnps) ;
p->chrom = strdup ("0") ; /* chromosome number not available from phase files */
p->sites = arrayCreate (4096, Site) ;
int i ; for (i = 0 ; i < p->N ; ++i) {
tc=fgetword(fp);
arrayp(p->sites,i,Site)->x = atoi (tc) ;
}
if (getc(fp) != '\n') die ("bad location line in phase file") ;
char var[2] ="S\0"; var[1] = 0 ; /*dummy variation line - used to create variationDict */
for (i = 0 ; i < p->N ; ++i)
{
if(version==1) *var = getc(fp) ;
dictAdd (variationDict, var, &(arrayp(p->sites,i,Site)->varD)) ; }
if(version==1) if (getc(fp) != '\n') die ("bad 5th line in phase file") ;
uchar **data = myalloc (p->N, uchar*) ;
for (i = 0 ; i < p->N ; ++i) data[i] = myalloc (p->M, uchar) ;
int j ; for (j = 0 ; j < p->M ; ++j)
{ for (i = 0 ; i < p->N ; ++i) data[i][j] = getc(fp) - '0' ;
if (getc(fp) != '\n') die ("bad %dth line in phase file", 7+j-version) ;
}
p->yz = arrayCreate(4096*32, uchar) ;
PbwtCursor *u = pbwtCursorCreate (p, TRUE, TRUE) ;
for (i = 0 ; i < p->N ; ++i)
{ for (j = 0 ; j < p->M ; ++j) u->y[j] = data[i][u->a[j]] ;
pbwtCursorWriteForwards (u) ;
if (nCheckPoint && !((i+1) % nCheckPoint)) pbwtCheckPoint (u, p) ;
}
pbwtCursorToAFend (u, p) ;
fprintf (logFile, "read phase file") ;
if (p->chrom) fprintf (logFile, " for chromosome %s", p->chrom) ;
fprintf (logFile, ": M, N are\t%d\t%d; yz length is %ld\n", p->M, p->N, arrayMax(p->yz)) ;
for (i = 0 ; i < p->N ; ++i) free(data[i]) ;
free (data) ; pbwtCursorDestroy (u) ;
return p ;
}
/*************** write haplotypes ******************/
void pbwtWriteHaplotypes (FILE *fp, PBWT *p)
{
int i, j, n = 0, M = p->M ;
uchar *hap = myalloc (M, uchar) ;
PbwtCursor *u = pbwtCursorCreate (p, TRUE, TRUE) ;
for (i = 0 ; i < p->N ; ++i)
{ for (j = 0 ; j < M ; ++j) hap[u->a[j]] = u->y[j] ;
for (j = 0 ; j < M ; ++j)
{ if (isWriteImputeRef && j > 0) putc (' ', fp) ;
putc (hap[j]?'1':'0', fp) ;
}
putc ('\n', fp) ; fflush (fp) ;
pbwtCursorForwardsRead (u) ;
}
free (hap) ; pbwtCursorDestroy (u) ;
fprintf (logFile, "written haplotype file: %d rows of %d\n", p->N, M) ;
}
void pbwtWriteTransposedHaplotypes (PBWT *p, FILE *fp)
{
int i, j ;
uchar **hap = pbwtHaplotypes (p) ;
for (j = 0 ; j < p->M ; ++j)
{ for (i = 0 ; i < p->N ; ++i)
putc (hap[j][i], fp) ;
putc ('\n', fp) ; fflush (fp) ;
}
for (i = 0 ; j < p->M ; ++j) free(hap[j]) ; free (hap) ;
fprintf (logFile, "written transposed haplotype file: %d rows of %d\n", p->M,p->N) ;
}
/*************** write IMPUTE files ********************/
void pbwtWriteImputeRef (PBWT *p, char *fileNameRoot)
{
FILE *fp ;
isWriteImputeRef = TRUE ;
if (!(fp=fopenTag (fileNameRoot, "imputeHaps","w"))) die ("can't open file") ;
pbwtWriteHaplotypes (fp, p) ; fclose (fp) ;
if (!(fp=fopenTag (fileNameRoot, "imputeLegend","w"))) die ("can't open file") ;
fprintf (fp, "rsID\tposition\ta0\ta1\n") ; /* header line */
pbwtWriteSites (p, fp) ; fclose (fp) ;
isWriteImputeRef = FALSE ;
}