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fastqtk.c
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fastqtk.c
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/* The MIT License
Copyright (c) 2010-2021 Daniel Nicorici <daniel.nicorici@gmail.com>
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.
*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#define BUFFER_SIZE 32 * 1024 * 1024
//define BUFFER_SIZE 32 * 1024 * 1024
//#define BUFFER_SIZE 3731
//maximum length of reads
#define MAX_LEN 32*1024
#define SIZE_OF_CHAR sizeof(char)
////////////////////////////////////////////////////////////////////////////////
const char CARS[] = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";
const int CARS_LEN = strlen(CARS);
const char newline = '\n';
char toCARS[256];
char DIGITS = 0;
char COUNTER[] = "----------------------------------------------------";
int COUNTER_LEN_MAX;
int COUNTER_LEN;
char EXTRA[100] = "\n";
void nextid(void) {
int n;
char x;
int i;
char flag;
if(COUNTER[0]!='@') {
// first call -- initialize
COUNTER_LEN_MAX = strlen(COUNTER);
for (i=0;i<256;i++) {
toCARS[i] = 0;
}
for (i=0;i<CARS_LEN;i++) {
toCARS[(int)CARS[i]] = (char) i + 1;
}
for (i=1;i<DIGITS+1;i++) {
COUNTER[i] = CARS[0];
}
n = strlen(EXTRA);
if (n == 1) {
COUNTER[i] = 10; // newline
COUNTER_LEN = DIGITS + 2;
} else if (n == 3 || n == 2) {
COUNTER[i++] = EXTRA[0];
COUNTER[i++] = EXTRA[1];
COUNTER[i] = 10; //newline
COUNTER_LEN = DIGITS + 4;
}
COUNTER[0] = (int) '@';
} else {
flag = 0;
if (COUNTER[1] == CARS[CARS_LEN-1]) {
flag = 1;
}
for (i=DIGITS;i>0;i--) {
x = toCARS[(int)COUNTER[i]];
if (x==CARS_LEN) {
COUNTER[i] = CARS[0];
} else {
COUNTER[i] = CARS[(int)x];
break;
}
}
if ((flag == 1) && (COUNTER[1] == CARS[0])) {
fprintf(stderr,"ERROR: Counter too small (%s)!",COUNTER);
exit(2);
}
}
}
////////////////////////////////////////////////////////////////////////////////
FILE* myfopen(char* filename, char* mode) {
FILE *ptr = fopen(filename, mode);
if (ptr == NULL) {
fprintf(stderr, "ERROR: Failed to open the file '%s'!\n",filename);
exit(2);
}
return ptr;
}
////////////////////////////////////////////////////////////////////////////////
char* mymalloc(size_t n)
{
char *ptr = (char *)malloc(SIZE_OF_CHAR * n);
if (ptr == NULL) {
fprintf(stderr, "ERROR: Failed to allocate memory!\n");
exit(2);
}
return ptr;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
int main(int argc, char * argv[])
{
char is_stdin = 0;
char is_stdout = 0;
char r1 = 0;
char end1 = 0;
char end2 = 0;
char len[MAX_LEN];
long long int u;
char *buffer;
char *b1;
char *b2;
char flag = 0;
char usage = 0;
char windows = 0;
size_t bytes_read,bytes_read1,bytes_read2,x;
size_t i,j,k,b1i,b2i,l;
size_t j1,j2,k1,k2,k1old,k2old;
long int threshold,trim,retain;
FILE *fip, *fr1, *fr2;
FILE *fop, *fi1p, *fi2p;
usage = 1;
if (argc > 1) {
if (strcmp(argv[1],"deinterleave") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk deinterleave <in.fq> <out1.fq> <out2.fq>\n\n");
fprintf(stderr, "It splits an interleaved input FASTQ file into two paired-end FASTQ files.\n");
fprintf(stderr, "For input from STDIN use - instead of <in.fq>.\n\n");
return 1;
} else {
usage = 2;
}
} else if (strcmp(argv[1],"interleave") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk interleave <in1.fq> <in2.fq> <out.fq>\n\n");
fprintf(stderr, "It interleaves two input paired-end FASTQ files into one output FASTQ file.\n");
fprintf(stderr, "For redirecting output to STDOUT use - instead of <out.fq>.\n\n");
return 1;
} else {
usage = 3;
}
} else if (strcmp(argv[1],"count") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk count <in.fq> <out.txt>\n\n");
fprintf(stderr, "It provides the total number of reads from an input FASTQ file and outputs it to a text file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 4;
}
} else if (strcmp(argv[1],"lengths") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk lengths <in.fq> <out.txt>\n\n");
fprintf(stderr, "It provides a summary statistics regarding the lengths of the reads from an input FASTQ file and outputs it to a text file.\n");
fprintf(stderr, "The output text file contains the unique lengths of the reads found in the input file, which are sorted in descending order.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 5;
}
} else if (strcmp(argv[1],"count-lengths") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk count-lengths <in.fq> <count.txt> <statistics.txt>\n\n");
fprintf(stderr, "It provides total number of reads and a summary statistics regarding the lengths of the reads from an input FASTQ file and outputs it to a text file.\n");
return 1;
} else {
usage = 6;
}
} else if (strcmp(argv[1],"tab-4") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk tab-4 <in.fq> <fastq.txt>\n\n");
fprintf(stderr, "It converts a FASTQ file into a tab-delimited text file with four columns.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 7;
}
} else if (strcmp(argv[1],"tab-8") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk tab-8 <in.fq> <fastq.txt>\n\n");
fprintf(stderr, "It converts an interleaved paired-end FASTQ file into a tab-delimited text file with 8 columns.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 8;
}
} else if (strcmp(argv[1],"detab") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk detab <fastq.txt> <out.fq>\n\n");
fprintf(stderr, "It converts a 4 or 8 columns text tab-delimited file into a FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 9;
}
} else if (strcmp(argv[1],"drop-short") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk drop-short <N> <in.fq> <out.fq>\n\n");
fprintf(stderr, "It drops the reads that have the sequences stricly shorter than N. N is a non-zero positive integer.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 10;
}
} else if (strcmp(argv[1],"NtoA") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk NtoA <in.fq> <out.fq>\n\n");
fprintf(stderr, "It replaces all the As from reads sequences with As in a FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 11;
}
} else if (strcmp(argv[1],"trim-5") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk trim-5 <N> <in.fq> <out.fq>\n\n");
fprintf(stderr, "It trims N nucleotides from 5' end of the reads from a FASTQ file. N is a non-zero positive integer.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 12;
}
} else if (strcmp(argv[1],"trim-3") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk trim-3 <N> <in.fq> <out.fq>\n\n");
fprintf(stderr, "It trims N nucleotides from 3' end of the reads from a FASTQ file. N is a non-zero positive integer.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 13;
}
} else if (strcmp(argv[1],"retain-5") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk retain-5 <N> <in.fq> <out.fq>\n\n");
fprintf(stderr, "It retains the first N nucleotides from 5' end of the reads from a FASTQ file. N is a non-zero positive integer.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 14;
}
} else if (strcmp(argv[1],"retain-3") == 0) {
if (argc != 5) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk retain-3 <N> <in.fq> <out.fq>\n\n");
fprintf(stderr, "It retains the last N nucleotides from 3' end of the reads from a FASTQ file. N is a non-zero positive integer.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 15;
}
} else if (strcmp(argv[1],"trim-id") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk trim-id <in.fq> <out.fq>\n\n");
fprintf(stderr, "It retains the beginning part of the reads ids all the way to the first blank space or newline. Basically the reads ids are\n");
fprintf(stderr, "truncated after the first blank space if they have one. Also the trims ids for the quality sequences (every third line is changed to +).\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 16;
}
} else if (strcmp(argv[1],"trim-poly") == 0) {
if (argc != 6) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk trim-poly <A|C|G|T|N|ACGT> <M> <in.fq> <out.fq>\n\n");
fprintf(stderr, "It trims poly-A/C/G/T/N tails at both ends of the reads sequences from a FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " * A|C|G|T|N|ACGT (nucleotide or nucleotides that form the poly tails that will be trimmed):\n");
fprintf(stderr, " A - poly-A tails are trimmed.\n");
fprintf(stderr, " C - poly-C tails are trimmed.\n");
fprintf(stderr, " G - poly-G tails are trimmed.\n");
fprintf(stderr, " T - poly-T tails are trimmed.\n");
fprintf(stderr, " N - poly-N tails are trimmed.\n");
fprintf(stderr, " ACGT - poly-A, poly-C, poly-G, and poly-T tails are trimmed.\n");
fprintf(stderr, " * M (the length of the poly tail; all poly-tails equal or longer than M will be trimmed).\n\n");
return 1;
} else {
usage = 17;
}
} else if (strcmp(argv[1],"compress-id") == 0) {
if (!(argc == 6 || argc == 5 || argc == 4)) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk compress-id [@|@@|/1|_1|/2|_2|/12|_12] [N|counts.txt] <in.fq> <out.fq>\n\n");
fprintf(stderr, "It does lossy compression on the reads ids from a FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " * N|counts.txt (count reads; if here is a dot then it is considered that a file has been given):\n");
fprintf(stderr, " N - number of reads in the input FASTQ file (or a much larger number). [500000].\n");
fprintf(stderr, " counts.txt - file that contains number of reads in the input FASTQ file <in.fq>, that was generated\n");
fprintf(stderr, " using 'fastqtk count in.fq counts.txt' beforehand.\n");
fprintf(stderr, " * @|@@|/1|_1|/2|_2|/12|_12 (settings for generating reads ids):\n");
fprintf(stderr, " @ - does NOT add /1 or /2 to reads ids. (FASTQ file is NOT interleaved) [DEFAULT]\n");
fprintf(stderr, " @@ - does NOT add /1 or /2 to reads ids. (FASTQ file is INTERLEAVED)\n\n");
fprintf(stderr, " /1 - adds /1 to the end of the reads ids. (FASTQ file is NOT interleaved)\n");
fprintf(stderr, " /2 - adds /2 to the end of the reads ids. (FASTQ file is NOT interleaved)\n");
fprintf(stderr, " /12 - adds /1 and /2 to the end of the reads ids. (FASTQ file is INTERLEAVED\n");
fprintf(stderr, " _1 - adds _1 to the end of the reads ids. (FASTQ file is NOT interleaved)\n");
fprintf(stderr, " _2 - adds _2 to the end of the reads ids. (FASTQ file is NOT interleaved)\n");
fprintf(stderr, " _12 - adds _1 and _2 to the end of the reads ids. (FASTQ file is INTERLEAVED)\n\n");
return 1;
} else {
usage = 19;
}
} else if (strcmp(argv[1],"drop-se") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk drop-se <in.fq> <out.fq>\n\n");
fprintf(stderr, "It drops the unparied reads from an interleaved FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 20;
}
} else if (strcmp(argv[1],"fq2fa") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk fq2fq <in.fq> <out.fa>\n\n");
fprintf(stderr, "It a FASTQ file to FASTA file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 21;
}
} else if (strcmp(argv[1],"fa2fq") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk fa2fq <in.fa> <out.fq>\n\n");
fprintf(stderr, "It a FASTA (generated using 'fastqtk fq2fa') file to FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 22;
}
} else if (strcmp(argv[1],"rev-com") == 0) {
if (argc != 4) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk rev-com <in.fq> <out.fq>\n\n");
fprintf(stderr, "It reverse complements all the reads from a FASTQ file.\n");
fprintf(stderr, "For redirecting to STDOUT/STDIN use - instead of file name.\n\n");
return 1;
} else {
usage = 23;
}
}
}
if (usage == 1) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: fastqtk <command> <arguments>\n");
fprintf(stderr, "Version: 0.28\n\n");
fprintf(stderr, "Command:\n");
fprintf(stderr, " interleave interleaves two paired-end FASTQ files.\n");
fprintf(stderr, " deinterleave splits an (already) interleaved (paired-end) FASTQ file.\n");
fprintf(stderr, " count counts all reads from a FASTQ file.\n");
fprintf(stderr, " lengths summary statistics for lengths of reads from a FASTQ file.\n");
fprintf(stderr, " count-lengths number of reads and summary statistics for lengths of reads from a FASTQ file.\n");
fprintf(stderr, " tab-4 converts a FASTQ file to a text tab-delimited file with 4 columns.\n");
fprintf(stderr, " tab-8 converts a (interleaved paired-end) FASTQ file to text tab-delimited file with 8 columns.\n");
fprintf(stderr, " detab converts a text tab-delimited file with 4/8 columns (converted using tab4/tab8) to FASTQ file.\n");
fprintf(stderr, " retain-5 retains the first N bp from 5'end of the reads from a FASTQ file.\n");
fprintf(stderr, " retain-3 retains the last N bp from 3'end of the reads from a FASTQ file.\n");
fprintf(stderr, " trim-5 trims 5' end of the reads from a FASTQ file.\n");
fprintf(stderr, " trim-3 trims 3' end of the reads from a FASTQ file.\n");
fprintf(stderr, " trim-id trims reads ids (removes everything after first space) from a FASTQ file.\n");
fprintf(stderr, " trim-poly trims poly-A/C/G/T/N tails at both ends of the reads sequences from a FASTQ file.\n");
fprintf(stderr, " drop-se drops unpaired reads from an interleaved paired-end FASTQ file.\n");
fprintf(stderr, " drop-short drops reads that have short sequences (below a given threshold).\n");
fprintf(stderr, " fq2fa converts a FASTQ file to FASTA file.\n");
fprintf(stderr, " fa2fq converts a FASTA file to FASTQ file.\n");
fprintf(stderr, " compress-id lossy compression of the reads ids from a FASTQ file.\n");
fprintf(stderr, " NtoA replaces all Ns in reads sequences with As in a FASTQ file.\n");
fprintf(stderr, " rev-com reverse complements all reads in a FASTQ file.\n");
fprintf(stderr, "\n");
return 1;
}
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
/*
DEINTERLEAVE
*/
if (usage == 2) {
is_stdin = 0;
if (strcmp(argv[2],"-")==0) {
fip = stdin;
is_stdin = 1;
} else {
fip = myfopen(argv[2],"r");
}
fr1 = myfopen(argv[3],"w");
fr2 = myfopen(argv[4],"w");
buffer = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
b1 = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
b2 = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
i = 0;
j = 0;
k = 0;
r1 = 0;
b1i = 0;
b2i = 0;
// for(;;)
while(1) {
bytes_read = fread(buffer, SIZE_OF_CHAR, BUFFER_SIZE, fip);
if (ferror(fip)) {
fprintf(stderr, "ERROR: Failed reading the input file.\n");
return 2;
}
if (bytes_read == 0 && feof(fip)) {
break;
}
if (feof(fip)) {
if(buffer[bytes_read-1] != '\n') {
bytes_read = bytes_read + 1;
buffer[bytes_read-1] = '\n';
} else if (bytes_read > 1 && buffer[bytes_read-2] == '\n' && buffer[bytes_read-1] == '\n') {
bytes_read = bytes_read - 1;
}
}
flag = 0;
for (i=0;i<bytes_read;i++) {
flag = 0;
if (buffer[i] == '\n') {
j = j + 1;
if (j==4) {
if (r1==0) {
l = i - k + 1;
memcpy(b1+b1i,buffer+k,l);
b1i = b1i + l;
r1 = 1;
} else {
l = i - k + 1;
memcpy(b2+b2i,buffer+k,l);
b2i = b2i + l;
r1 = 0;
}
j = 0;
k = i + 1;
}
}
}
if (flag == 0) {
i = bytes_read - 1;
if(r1 == 0){
l = i - k + 1;
memcpy(b1+b1i,buffer+k,l);
b1i = b1i + l;
} else {
l = i - k + 1;
memcpy(b2+b2i,buffer+k,l);
b2i = b2i + l;
}
}
fwrite(b1, SIZE_OF_CHAR, b1i, fr1);
fwrite(b2, SIZE_OF_CHAR, b2i, fr2);
b1i = 0;
b2i = 0;
k = 0;
}
if (is_stdin == 0) {
fclose(fip);
}
fclose(fr1);
fclose(fr2);
free(buffer);
free(b1);
free(b2);
return 0;
} // end DEINTERLEAVE
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
/*
INTERLEAVE
*/
if (usage == 3) {
is_stdout = 0;
if (strcmp(argv[4],"-")==0) {
fop = stdout;
is_stdout = 1;
} else {
fop = myfopen(argv[4],"w");
}
fi1p = myfopen(argv[2],"r");
fi2p = myfopen(argv[3],"r");
buffer = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
b1 = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
b2 = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
i = 0;
j = 0;
j1 = 0;
j2 = 0;
k = 0;
k1 = 0;
k1old = 0;
k2 = 0;
k2old = 0;
r1 = 0;
b1i = 0;
b2i = 0;
bytes_read1 = 0;
bytes_read2 = 0;
end1 = 0;
end2 = 0;
while(1) {
if (end1 == 1 && end2 == 1) {
break;
}
////////////////////////////////////////
if (r1 == 0) {
if (k1 == 0) {
bytes_read1 = fread(b1, SIZE_OF_CHAR, BUFFER_SIZE, fi1p);
if (ferror(fi1p)) {
fprintf(stderr, "ERROR: Failed reading the input file.\n");
return 2;
}
if (bytes_read1 == 0 && feof(fi1p)) {
end1 = 1;
r1 = 1;
continue;
}
if (feof(fi1p)) {
if(b1[bytes_read1-1] != '\n') {
bytes_read1 = bytes_read1 + 1;
b1[bytes_read1-1] = '\n';
} else if (bytes_read1 > 1 && b1[bytes_read1-2] == '\n' && b1[bytes_read1-1] == '\n') {
bytes_read1 = bytes_read1 - 1;
}
}
}
flag = 0;
for (i=k1;i<bytes_read1;i++) {
flag = 0;
if (b1[i] == '\n') {
j1 = j1 + 1;
if (j1==4) {
flag = 1;
j1 = 0;
k1old = k1;
k1 = i + 1;
break;
}
}
}
if (flag == 0) {
k1old = k1;
k1 = bytes_read1;
r1 = 0;
// read more
} else {
r1 = 1;
}
l = k1 - k1old;
if(BUFFER_SIZE < k + l + 10) {
// empty the buffer
fwrite(buffer, SIZE_OF_CHAR, k, fop);
k = 0;
}
memcpy(buffer+k,b1+k1old,l);
k = k + l;
if (flag == 0 || k1 == bytes_read1) {
k1 = 0;
k1old = 0;
}
////////////////////////////////////////////////////////////////
} else {
if (k2 == 0) {
bytes_read2 = fread(b2, SIZE_OF_CHAR, BUFFER_SIZE, fi2p);
if (ferror(fi2p)) {
fprintf(stderr, "ERROR: Failed reading the input file.\n");
return 2;
}
if (bytes_read2 == 0 && feof(fi2p)) {
end2 = 1;
r1 = 0;
continue;
}
if (feof(fi2p)) {
if(b2[bytes_read2-1] != '\n') {
bytes_read2 = bytes_read2 + 1;
b2[bytes_read2-1] = '\n';
} else if (bytes_read2 > 1 && b2[bytes_read2-2] == '\n' && b2[bytes_read2-1] == '\n') {
bytes_read2 = bytes_read2 - 1;
}
}
}
flag = 0;
for (i=k2;i<bytes_read2;i++) {
flag = 0;
if (b2[i] == '\n') {
j2 = j2 + 1;
if (j2==4) {
flag = 1;
j2 = 0;
k2old = k2;
k2 = i + 1;
break;
}
}
}
if (flag == 0) {
k2old = k2;
k2 = bytes_read2;
r1 = 1;
// read more
} else {
r1 = 0;
}
l = k2 - k2old;
if(BUFFER_SIZE < k + l + 10) {
fwrite(buffer, SIZE_OF_CHAR, k, fop);
k = 0;
}
memcpy(buffer+k,b2+k2old,l);
k = k + l;
if (flag == 0 || k2 == bytes_read2) {
k2 = 0;
k2old = 0;
}
}
}
if (k!=0) {
fwrite(buffer, SIZE_OF_CHAR, k, fop);
}
if (is_stdout==0) {
fclose(fop);
}
fclose(fi1p);
fclose(fi2p);
free(buffer);
free(b1);
free(b2);
return 0;
} // end INTERLEAVE
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
/*
COUNT
*/
if (usage == 4) {
is_stdin = 0;
if (strcmp(argv[2],"-")==0) {
fip = stdin;
is_stdin = 1;
} else {
fip = myfopen(argv[2],"r");
}
is_stdout = 0;
if (strcmp(argv[3],"-")==0) {
fop = stdout;
is_stdout = 1;
} else {
fop = myfopen(argv[3],"w");
}
buffer = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
u = 0;
// for(;;)
while(1) {
bytes_read = fread(buffer, SIZE_OF_CHAR, BUFFER_SIZE, fip);
if (ferror(fip)) {
fprintf(stderr, "ERROR: Failed reading the input file.\n");
return 2;
}
if (bytes_read == 0 && feof(fip)) {
break;
}
if (feof(fip)) {
if(buffer[bytes_read-1] != '\n') {
bytes_read = bytes_read + 1;
buffer[bytes_read-1] = '\n';
} else if (bytes_read > 1 && buffer[bytes_read-2] == '\n' && buffer[bytes_read-1] == '\n') {
bytes_read = bytes_read - 1;
}
}
for (i=0;i<bytes_read;i++) {
if (buffer[i] == '\n') {
u = u + 1;
}
}
}
if ( u%4 == 0) {
u = u/4;
} else {
if (u>2) {
u = u/4 + 1;
} else {
u = 0;
}
}
fprintf(fop,"%lld\n",u);
if (is_stdin == 0) {
fclose(fip);
}
if (is_stdout == 0) {
fclose(fop);
}
free(buffer);
return 0;
} // end COUNT
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
/*
LENGTHS
*/
if (usage == 5) {
is_stdin = 0;
if (strcmp(argv[2],"-")==0) {
fip = stdin;
is_stdin = 1;
} else {
fip = myfopen(argv[2],"r");
}
is_stdout = 0;
if (strcmp(argv[3],"-")==0) {
fop = stdout;
is_stdout = 1;
} else {
fop = myfopen(argv[3],"w");
}
buffer = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
for (i=0;i<MAX_LEN;i++) {
len[i] = 0;
}
j = 2;
k = 0;
l = 0;
windows = 0;
// for(;;)
while(1) {
bytes_read = fread(buffer, SIZE_OF_CHAR, BUFFER_SIZE, fip);
if (ferror(fip)) {
fprintf(stderr, "ERROR: Failed reading the input file.\n");
return 2;
}
if (bytes_read == 0 && feof(fip)) {
break;
}
flag = 0;
for (i=0;i<bytes_read;i++) {
if (buffer[i] == '\n') {
j = j + 1;
if (j==3) {
k = i;
flag = 1;
} else if (j==4) {
l = l + i - k - 1;
if (l < MAX_LEN && l - 1 > 0) {
len[l] = 1;
} else {
fprintf(stderr, "ERROR: Too long read sequence found. Maximum length of supported reads is %d.\n",MAX_LEN);
free(buffer);
return 2;
}
j = 0;
l = 0;
flag = 0;
}
}
}
if (flag == 1) {
flag = 0;
i = bytes_read;
l = i - k - 1;
k = 0;
}
if (k != 0 && k != 1 && buffer[k-1] == '\r') {
windows = 1;
}
}
for (i=MAX_LEN-1;i>0;i--) {
if (len[i] != 0) {
fprintf(fop,"%ld\n",i-windows);
}
}
if (len[0] != 0 && windows == 0) {
fprintf(fop,"0\n");
}
if (is_stdin == 0) {
fclose(fip);
}
if (is_stdout == 0) {
fclose(fop);
}
free(buffer);
return 0;
} // end LENGTHS
////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////
/*
COUNT-LENGTHS
*/
if (usage == 6) {
is_stdin = 0;
if (strcmp(argv[2],"-")==0) {
fip = stdin;
is_stdin = 1;
} else {
fip = myfopen(argv[2],"r");
}
fr1 = myfopen(argv[3],"w");
fr2 = myfopen(argv[4],"w");
buffer = mymalloc(BUFFER_SIZE * SIZE_OF_CHAR + 1);
for (i=0;i<MAX_LEN;i++) {
len[i] = 0;
}
u = 0;
j = 2;
k = 0;
l = 0;
windows = 0;
// for(;;)
while(1) {
bytes_read = fread(buffer, SIZE_OF_CHAR, BUFFER_SIZE, fip);
if (ferror(fip)) {
fprintf(stderr, "ERROR: Failed reading the input file.\n");
return 2;
}
if (bytes_read == 0 && feof(fip)) {
break;
}
flag = 0;
for (i=0;i<bytes_read;i++) {
if (buffer[i] == '\n') {
j = j + 1;
u = u + 1;
if (j==3) {
k = i;
flag = 1;
} else if (j==4) {
l = l + i - k - 1;
if (l<MAX_LEN) {