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trtr.c
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trtr.c
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/**********************************************************************
* TRTR: Trim Reads of Tandem Repeats
* Copyright (C) 2014 Jonathan Richards
*
* This program 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 2 of the License, or
* (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* Written by Jonathan Richards, [email protected]
*
* Special thanks to my advisor, Professor Alison Gammie, for bringing
* this problem to my attention and to my reseach partner, Mitchell
* Vollger, for help testing and finalizing.
**********************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <stdbool.h>
#include <sys/types.h>
#include <assert.h>
#include <errno.h>
//use my getline for portability
//adapted from getline.c written by Jan Brittenson, [email protected]
//http://www.opensource.apple.com/source/cvs/cvs-19/cvs/lib/getline.c
ssize_t getline(char** lineptr, size_t* n, FILE* stream) {
size_t nchars_avail;
char* read_pos;
int save_errno;
ssize_t ret;
register int c;
if (!lineptr || !n || !stream) {
errno = EINVAL;
return -1;
}
if (!*lineptr) {
*n = 128;
*lineptr = malloc(*n);
if (!*lineptr) {
errno = ENOMEM;
return -1;
}
}
nchars_avail = *n;
read_pos = *lineptr;
for (;;) {
c = getc(stream);
save_errno = errno;
if (c != '\r') { //for portability...
assert((*lineptr+*n)==(read_pos+nchars_avail));
if (nchars_avail < 2) {
*n *= 2;
nchars_avail = *n + *lineptr - read_pos;
*lineptr = realloc(*lineptr, *n);
if (!*lineptr) {
errno = ENOMEM;
return -1;
}
read_pos = *n - nchars_avail + *lineptr;
assert((*lineptr+*n) == (read_pos+nchars_avail));
}
if (ferror(stream)) {
errno = save_errno;
return -1;
}
if (c == EOF) {
if (read_pos == *lineptr)
return -1;
else
break;
}
*read_pos++ = c;
nchars_avail--;
if (c == '\n')
break;
}
}
*read_pos = '\0';
ret = read_pos - *lineptr;
return ret;
}
int main(int argc, char *argv[]) {
char *line = NULL;
size_t len = 0;
ssize_t line_length;
int count = 0;
size_t leftTrim = 0;
size_t rightTrim = 0;
size_t i;
size_t i_max = 10;
size_t j;
size_t r;
size_t length;
size_t longest_region;
char *ptr;
bool matched = false;
bool aggressive_trim = true;
FILE *file = fopen(argv[1], "r");
if (argc >= 3) {
i_max = strtol(argv[2], &ptr, 10);
if (argc >= 4) {
aggressive_trim = strtol(argv[3], &ptr, 10);
}
}
if (file != NULL) {
while ((line_length = getline(&line, &len, file)) != -1) {
count++;
switch (count) {
//read name
case 1:
fputs(line, stdout);
break;
//read sequence
case 2:
//find leftTrim
longest_region = 0;
for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat
if (line[0] == line[i]) {
matched = true;
j=1;
r=0;
while (matched == true) {
if (j == i) {
r++;
j=0;
} else if (line[j] != line[(r+1)*i+j]) {
//no length comparison needed because of \n at end
matched = false;
if (aggressive_trim) {
length = r*i+j;
} else {
length = r*i;
}
if (length > longest_region && r>0) {
longest_region = length;
}
} else {
j++;
}
}
}
}
leftTrim = longest_region;
//find rightTrim
longest_region = 0;
for (i=1; i<=i_max && i<=line_length/2; i++) { //size of repeat
if (line[line_length-2] == line[line_length-2-i]) {
matched = true;
j=1;
r=0;
while (matched == true) {
if (j == i) {
r++;
j=0;
} else if ((line[line_length-2-j] != line[line_length-2-(r+1)*i-j])
|| line_length-2-(r+1)*i-j == leftTrim) {
matched = false;
if (aggressive_trim) {
length = r*i+j;
} else {
length = r*i;
}
if (length > longest_region && r>0) {
longest_region = length;
}
} else {
j++;
}
}
}
}
rightTrim = line_length-longest_region-1;
//print trimmed line
line[rightTrim] = '\n';
line[rightTrim+1] = '\0';
fputs(line+leftTrim, stdout);
break;
//+
case 3:
fputs(line, stdout);
break;
//read qualities
case 4:
count = 0; //reset to read title
line[rightTrim] = '\n';
line[rightTrim+1] = '\0';
fputs(line+leftTrim, stdout);
break;
default:
break;
}
}
free(line);
fclose(file);
} else {
perror(argv[1]);
}
return 0;
}