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seqio.c
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seqio.c
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/* File: seqio.c
* Author: Richard Durbin ([email protected])
* Copyright (C) Richard Durbin, Cambridge University, 2018
*-------------------------------------------------------------------
* Description: buffered package to read arbitrary sequence files - much faster than readseq
* Exported functions:
* HISTORY:
* Last edited: Dec 27 11:15 2018 (rd109)
* Created: Fri Nov 9 00:21:21 2018 (rd109)
*-------------------------------------------------------------------
*/
#include "seqio.h"
SeqIO *seqIOopen (char *filename, int* convert, BOOL isQual)
{
SeqIO *si = new0 (1, SeqIO) ;
if (!strcmp (filename, "-")) si->f = gzdopen (fileno (stdin), "r") ;
else si->f = gzopen (filename, "r") ;
if (!si->f) { free(si) ; return 0 ; }
si->bufSize = 1<<24 ;
si->b = si->buf = new (si->bufSize, char) ;
si->convert = convert ;
si->isQual = isQual ;
si->nb = gzread (si->f, si->buf, si->bufSize) ;
if (!si->nb)
{ fprintf (stderr, "sequence file %s unreadable or empty\n", filename) ;
seqIOclose (si) ;
return 0 ;
}
si->line = 1 ;
if (*si->buf == '>')
{ si->type = FASTA ; si->isQual = FALSE ;
if (!si->convert) si->convert = dna2textAmbigConv ; /* default: need to remove whitespace */
}
else if (*si->buf == '@') si->type = FASTQ ;
else if (*si->buf == 'B')
{ si->type = BINARY ;
if (si->nb <= 8) die ("binary file too short\n") ;
si->qualThresh = si->buf[1] ;
si->isQual = (si->qualThresh > 0) ;
si->nSeq = *(U64*)si->buf & 0xffffffffffffLL ; /* 6 bytes of ff */
si->b += 8 ; si->nb -= 8 ;
}
else
{ fprintf (stderr, "sequence file %s is unknown type\n", filename) ;
seqIOclose (si) ;
return 0 ;
}
return si ;
}
void seqIOclose (SeqIO *si)
{ free (si->buf) ;
if (si->seqBuf) free (si->seqBuf) ; if (si->qualBuf) free (si->qualBuf) ;
gzclose (si->f) ;
free (si) ;
}
/********** local routines for seqIOread() ***********/
static int bufRefill (SeqIO *si)
{ si->b -= si->recStart ; /* will be position after move */
memmove (si->buf, si->buf + si->recStart, si->b - si->buf) ;
si->idStart -= si->recStart ; si->descStart -= si->recStart ; /* adjust all the offsets */
si->seqStart -= si->recStart ; si->qualStart -= si->recStart ;
si->recStart = 0 ;
si->nb = gzread (si->f, si->b, si->buf + si->bufSize - si->b) ;
return si->nb ;
}
static int bufExtend (SeqIO *si)
{
char *newbuf = new (si->bufSize*2, char) ;
memcpy (newbuf, si->buf, si->bufSize) ;
free (si->buf) ; si->buf = newbuf ;
si->b = si->buf + si->bufSize ; si->nb = si->bufSize ;
si->nb = gzread (si->f, si->b, si->bufSize) ;
si->bufSize *= 2 ;
return si->nb ;
}
#define bufAdvanceEndRecord(si) \
{ ++si->b ; \
if (!--si->nb) \
{ if (si->recStart) bufRefill (si) ; \
else if (si->b == si->buf + si->bufSize) bufExtend (si) ; \
} \
}
#define bufAdvanceInRecord(si) \
{ bufAdvanceEndRecord(si) ; \
if (!si->nb) \
{ fprintf (stderr, "incomplete sequence record line %d\n", si->line) ; return FALSE ; } \
}
#define bufConfirmNbytes(si, n) \
{ if (si->nb < n && si->recStart) bufRefill (si) ; \
if (si->nb < n && si->b == si->buf + si->bufSize) bufExtend (si) ; \
if (si->nb < n) \
{ fprintf (stderr, "incomplete sequence record line %d\n", si->line) ; return FALSE ; } \
}
#include <ctype.h>
BOOL seqIOread (SeqIO *si)
{
if (!si->nb) return FALSE ;
si->recStart = si->b - si->buf ;
if (si->type == BINARY)
{ bufConfirmNbytes (si, 3*sizeof(int)) ;
si->idLen = *((int*)si->b) ; si->b += sizeof(int) ;
si->descLen = *((int*)si->b) ; si->b += sizeof(int) ;
si->seqLen = *((int*)si->b) ; si->b += sizeof(int) ;
si->nb -= 3*sizeof(int) ;
int nBytes = si->idLen+1 + si->descLen+1
+ (si->seqLen+3)/4 + si->isQual ? (si->seqLen+7)/8 : 0 ;
nBytes = 4*((nBytes+3)/4) ;
bufConfirmNbytes (si, nBytes) ;
si->idStart = si->b - si->buf ;
si->descStart = si->idStart + si->idLen+1 ;
if (si->seqLen > si->seqBufSize)
{ if (si->seqBufSize) { free (si->seqBuf) ; if (si->isQual) free (si->qualBuf) ; }
si->seqBufSize = 1 << 20 ; while (si->seqBufSize < si->seqLen) si->seqBufSize <<= 1 ;
si->seqBuf = new (si->seqBufSize, char) ;
if (si->isQual) si->qualBuf = new (si->seqBufSize, char) ;
}
si->seqStart = si->descStart + si->descLen+1 ;
sqioSeqUnpack ((U8*)(si->buf+si->seqStart), si->seqBuf, si->seqLen) ;
if (si->isQual)
{ si->qualStart = si->seqStart + (si->seqLen+3)/4 ;
sqioQualUnpack ((U8*)(si->buf+si->qualStart), si->qualBuf, si->seqLen, si->qualThresh) ;
}
++si->nSeq ;
si->b += nBytes ; si->nb -= nBytes ;
return TRUE ;
}
/* if get to here then this is a text file, FASTA or FASTQ */
if (si->type == FASTA)
{ if (*si->b != '>') die ("no initial > for FASTA record line %d", si->line) ; }
else if (si->type == FASTQ)
{ if (*si->b != '@') die ("no initial @ for FASTQ record line %d", si->line) ; }
bufAdvanceInRecord(si) ; si->idStart = si->b - si->buf ;
while (!isspace(*si->b)) bufAdvanceInRecord(si) ;
si->idLen = si->b - sqioId(si) ;
if (*si->b != '\n') /* a space or tab - whatever follows on this line is description */
{ *si->b = 0 ; bufAdvanceInRecord(si) ;
si->descStart = si->b - si->buf ;
while (*si->b != '\n') bufAdvanceInRecord(si) ;
si->descLen = si->b - sqioDesc(si) ;
}
else { si->descLen = si->descStart = 0 ; }
*si->b = 0 ;
++si->line ; bufAdvanceInRecord(si) ; /* line 2 */
si->seqStart = si->b - si->buf ;
if (si->type == FASTA)
{ while (si->nb && *si->b != '>')
{ while (*si->b != '\n') bufAdvanceInRecord(si) ;
++si->line ; bufAdvanceEndRecord(si) ;
}
char *s = sqioSeq(si), *t = s ;
while (s < si->b) if ((*t++ = si->convert[*s++]) < 0) --t ;
si->seqLen = t - sqioSeq(si) ;
}
else if (si->type == FASTQ)
{ while (*si->b != '\n') bufAdvanceInRecord(si) ;
si->seqLen = si->b - sqioSeq(si) ;
if (si->convert)
{ char *s = sqioSeq(si) ;
while (s < si->b) { *s = si->convert[*s] ; ++s ; }
}
++si->line ; bufAdvanceInRecord(si) ; /* line 3 */
if (*si->b != '+') die ("missing + FASTQ line %d", si->line) ;
while (*si->b != '\n') bufAdvanceInRecord(si) ; /* ignore remainder of + line */
++si->line ; bufAdvanceInRecord(si) ; /* line 4 */
si->qualStart = si->b - si->buf ;
while (*si->b != '\n') bufAdvanceInRecord(si) ;
if (si->b - si->buf - si->qualStart != si->seqLen)
die ("qual not same length as seq line %d", si->line) ;
if (si->isQual) { char *q = sqioQual(si), *e = q + si->seqLen ; while (q < e) *q++ -= 33 ; }
++si->line ; bufAdvanceEndRecord(si) ;
}
++si->nSeq ;
return TRUE ;
}
/* something for the future? */
SeqIO *seqIObinaryOpen (char *filename, int nSeq) ; /* n = 0 if number unknown */
void seqIObinaryWrite (SeqIO *si) ;
/********** some routines to pack sequence and qualities **************/
void sqioSeqPack (char *s, U8 *u, int len) /* compress s into (len+3)/4 u */
{
int i ;
while (len > 4)
{ *u = 0 ; for (i = 0 ; i < 4 ; ++i) *u = (*u << 2) | dna2indexConv[*s++] ;
len -= 4 ; ++u ;
}
if (len) { *u = 0 ; for (i = 0 ; i < len ; ++i) *u = (*u << 2) | dna2indexConv[*s++] ; }
}
void sqioSeqUnpack (U8 *u, char *s, int len) /* uncompress (len+3)/4 u into s */
{
int i ;
while (len > 4)
{ for (i = 4 ; i-- ; ) { s[i] = (*u & 0x3) ; *u >>= 2 ; }
len -= 4 ; ++u ; s += 4 ;
}
if (len) for (i = len ; --i ; ) { s[i] = (*u & 0x3) ; *u >>= 2 ; }
}
void sqioQualPack (char *q, U8 *u, int len, int thresh) /* compress q into (len+7)/8 u */
{
int i ;
while (len > 8)
{ *u = 0 ; for (i = 0 ; i < 8 ; ++i) { if (*q++ >= thresh) *u |= 1 ; *u <<= 1 ; }
len -= 8 ; ++u ;
}
if (len) { *u = 0 ; for (i = 0 ; i < len ; ++i) { if (*q++ >= thresh) *u |= 1 ; *u <<= 1 ; } }
}
void sqioQualUnpack (U8 *u, char *q, int len, int thresh) /* uncompress (len+7)/8 u into q */
{
int i ;
while (len > 8)
{ for (i = 8 ; i-- ; ) { q[i] = (*u & 0x1) ? thresh : 0 ; *u >>= 1 ; }
len -= 8 ; ++u ; q += 8 ;
}
if (len) for (i = len ; --i ; ) { q[i] = (*u & 0x1) ? thresh : 0 ; *u >>= 1 ; }
}
/*********** standard conversion tables **************/
int dna2textConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', -2, 'C', -2, -2, -2, 'G', -2, -2, -2, -2, -2, -2, 'N', -2,
-2, -2, -2, -2, 'T', -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', -2, 'C', -2, -2, -2, 'G', -2, -2, -2, -2, -2, -2, 'N', -2,
-2, -2, -2, -2, 'T', -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int dna2textAmbigConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, '-', -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', 'B', 'C', 'D', -2, -2, 'G', 'H', -2, -2, 'K', -2, 'M', 'N', -2,
-2, -2, 'R', 'S', 'T', -2, 'V', 'W', -2, 'Y', -2, -2, -2, -2, -2, -2,
-2, 'A', 'B', 'C', 'D', -2, -2, 'G', 'H', -2, -2, 'K', -2, 'M', 'N', -2,
-2, -2, 'R', 'S', 'T', -2, 'V', 'W', -2, 'Y', -2, -2, -2, -2, -2, -2,
} ;
int dna2textAmbig2NConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', 'N', 'C', 'N', -2, -2, 'G', 'N', -2, -2, 'N', -2, 'N', 'N', -2,
-2, -2, 'N', 'N', 'T', -2, 'N', 'N', -2, 'N', -2, -2, -2, -2, -2, -2,
-2, 'A', 'N', 'C', 'N', -2, -2, 'G', 'N', -2, -2, 'N', -2, 'N', 'N', -2,
-2, -2, 'N', 'N', 'T', -2, 'N', 'N', -2, 'N', -2, -2, -2, -2, -2, -2,
} ;
int dna2indexConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 0, -2, 1, -2, -2, -2, 2, -2, -2, -2, -2, -2, -2, 4, -2,
-2, -2, -2, -2, 3, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 0, -2, 1, -2, -2, -2, 2, -2, -2, -2, -2, -2, -2, 4, -2,
-2, -2, -2, -2, 3, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int dna2binaryConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 1, -2, 2, -2, -2, -2, 4, -2, -2, -2, -2, -2, -2, 15, -2,
-2, -2, -2, -2, 8, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 1, -2, 2, -2, -2, -2, 4, -2, -2, -2, -2, -2, -2, 15, -2,
-2, -2, -2, -2, 8, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int dna2binaryAmbigConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, 0, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 1, 14, 2, 13, -2, -2, 4, 11, -2, -2, 12, -2, 3, 15, -2,
-2, -2, 5, 6, 8, -2, 7, 9, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 1, 14, 2, 13, -2, -2, 4, 11, -2, -2, 12, -2, 3, 15, -2,
-2, -2, 5, 6, 8, -2, 7, 9, -2, -2, -2, -2, -2, -2, -2, -2,
} ;
int aa2textConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 'A', 'X', 'C', 'D', 'E', 'F', 'G', 'H', 'I', -2, 'K', 'L', 'M', 'N', -2,
'P', 'Q', 'R', 'S', 'T', -2, 'V', 'W', 'X', 'Y', 'X', -2, -2, -2, -2, -2,
-2, 'A', 'X', 'C', 'D', 'E', 'F', 'G', 'H', 'I', -2, 'K', 'L', 'M', 'N', -2,
'P', 'Q', 'R', 'S', 'T', -2, 'V', 'W', 'X', 'Y', 'X', -2, -2, -2, -2, -2,
} ;
int aa2indexConv[] = {
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2,
-2, 0, 20, 1, 2, 3, 4, 5, 6, 7, -2, 8, 9, 10, 11, -2,
12, 13, 14, 15, 16, -2, 17, 18, 20, 19, 20, -2, -2, -2, -2, -2,
-2, 0, 20, 1, 2, 3, 4, 5, 6, 7, -2, 8, 9, 10, 11, -2,
12, 13, 14, 15, 16, -2, 17, 18, 20, 19, 20, -2, -2, -2, -2, -2,
} ;
int noConv[] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127
} ;
/******** end of file ********/