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read_util.c
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read_util.c
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/*
* read_util.c: Utility functions for processing reads
*/
/*
* Copyright (C) 2012 Tanja Magoc
* Copyright (C) 2012, 2013, 2014 Eric Biggers
*
* This file is part of FLASH, a fast tool to merge overlapping paired-end
* reads.
*
* FLASH is free software; you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free
* Software Foundation; either version 3 of the License, or (at your option)
* any later version.
*
* FLASH is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more
* details.
*
* You should have received a copy of the GNU General Public License
* along with FLASH; if not, see http://www.gnu.org/licenses/.
*/
#include "read.h"
#include "iostream.h"
#include "util.h"
#include <assert.h>
#include <ctype.h>
#include <string.h>
/*
* A table mapping ASCII characters (actually, 8-bit bytes) to "canonical" form
* for base processing:
*
* a, A => A
* c, C => C
* g, G => G
* t, T => T
* everything else => N
*/
static const char canonical_ascii_tab[256] = {
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', /* A */ 'A', 'N', /* C */ 'C', 'N', 'N', 'N', /* G */ 'G',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', /* T */ 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', /* a */ 'A', 'N', /* c */ 'C', 'N', 'N', 'N', /* g */ 'G',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', /* t */ 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N',
};
/* Turns lowercase a, c, g, t into uppercase;
* uppercase A, C, G, T stay the same;
* everything else turns into 'N'. */
static inline char
canonical_ascii_char(char c)
{
return canonical_ascii_tab[(unsigned char)c];
}
/* A table mapping an ASCII base character in canonical form to its complement.
* Unknown bases (N's) stay unknown. */
static const char complement_tab[] = {
['A'] = 'T',
['C'] = 'G',
['G'] = 'C',
['T'] = 'A',
['N'] = 'N',
};
/* Complements a canonical ASCII base (A, C, G, T, N). */
static inline char
complement(char c)
{
return complement_tab[(unsigned char)c];
}
static inline char
identity_mapping(char c)
{
return c;
}
/* Reverse a sequence of @len chars, applying the mapping function @map_char to
* each, including the middle char if @len is odd. */
static inline void
reverse_with_mapping(char *p, size_t len, char (*map_char)(char))
{
char tmp;
char *pp = p + len;
while (pp > p) {
--pp;
tmp = *p;
*p = (*map_char)(*pp);
*pp = (*map_char)(tmp);
++p;
}
}
/* Reverse-complement a read in place. */
void
reverse_complement(struct read *r)
{
reverse_with_mapping(r->seq, r->seq_len, complement);
reverse_with_mapping(r->qual, r->seq_len, identity_mapping);
}
/* Remove all whitespace from the end of the line/string. Return the length of
* the trimmed string. */
static inline int
trim(char *s, int len)
{
while (len > 0 && isspace((unsigned char)s[len - 1]))
s[--len] = '\0';
return len;
}
void
clean_read(struct read *r, int phred_offset, struct input_stream *in,
uint64_t line_no)
{
int seq_len;
char *seq;
char *qual;
r->seq_len = trim(r->seq, r->seq_len);
r->tag_len = trim(r->tag, r->tag_len);
r->qual_len = trim(r->qual, r->qual_len);
seq_len = r->seq_len;
if (r->qual_len != seq_len) {
fatal_error("Qual string length (%d) not the same as sequence "
"length (%d) (file \"%s\", near line %"PRIu64")",
r->qual_len, seq_len,
input_stream_get_name(in), line_no);
}
seq = r->seq;
for (int i = 0; i < seq_len; i++) {
if (isspace((unsigned char)seq[i])) {
fatal_error("Invalid sequence string: "
"contains whitespace "
"(file \"%s\", near line %"PRIu64")",
input_stream_get_name(in), line_no);
}
seq[i] = canonical_ascii_char(seq[i]);
}
qual = r->qual;
if (phred_offset > 0) {
for (int i = 0; i < seq_len; i++) {
if (qual[i] < phred_offset) {
fatal_error("Qual string contains character "
"under phred_offset = %d "
"(file \"%s\", near line %"PRIu64")",
phred_offset,
input_stream_get_name(in), line_no);
}
qual[i] -= phred_offset;
}
}
}
void
clean_read_for_write(struct read *r, int phred_offset)
{
assert(r->seq_len == r->qual_len);
if (phred_offset > 0) {
char *qual = r->qual;
int qual_len = r->qual_len;
for (int i = 0; i < qual_len; i++)
qual[i] += phred_offset;
}
}
void
copy_tag(struct read *to, const struct read *from)
{
if (to->tag_bufsz < from->tag_len + 1) {
to->tag = xrealloc(to->tag, from->tag_len + 1);
to->tag_bufsz = from->tag_len + 1;
}
to->tag_len = from->tag_len;
memcpy(to->tag, from->tag, from->tag_len + 1);
}
/*
* Given the FASTQ tags of two paired-end reads, find the FASTQ tag to give to
* the combined read.
*
* This is done by stripping off the characters trailing the '/' (e.g. "/1" and
* "/2"), unless there is a "barcode" beginning with the '#' character, which is
* kept.
*/
void
get_combined_tag(const struct read *read_1,
const struct read *read_2,
struct read *combined_read)
{
char *p;
copy_tag(combined_read, read_1);
for (p = &combined_read->tag[combined_read->tag_len - 1];
p >= combined_read->tag;
p--)
{
if (*p == '/') {
/* Tags are different, and there's a forward slash in
* the first tag. Remove everything after the forward
* slash, unless there's a barcode, which we keep. */
if (*(p + 1) != '\0' && *(p + 2) == '#') {
/* read ID has a barcode. */
do {
*p = *(p + 2);
} while (*(++p + 2) != '\0');
}
*p = '\0';
combined_read->tag_len = p - combined_read->tag;
break;
}
}
}