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Release 1.0
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@ezorita
ezorita committed Dec 2, 2014
1 parent 5783cab commit 746edb6
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Showing 8 changed files with 87 additions and 60 deletions.
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -10,3 +10,5 @@ starcode
test/analysis.txt
test/.inspect.gdb
test/runtests
doc/*.log
*\#*
5 changes: 4 additions & 1 deletion .travis.yml
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Expand Up @@ -2,4 +2,7 @@ language: c
compiler:
- gcc
- clang
script: make
branches:
only:
- master
script: make && cd test && make test
2 changes: 0 additions & 2 deletions src/_starcode.h
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Expand Up @@ -5,8 +5,6 @@
** Guillaume Filion (guillaume.filion@gmail.com)
** Eduard Valera Zorita (ezorita@mit.edu)
**
** Last modified: July 8, 2014
**
** License:
** 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
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23 changes: 23 additions & 0 deletions src/_trie.h
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@@ -1,3 +1,26 @@
/*
** Copyright 2014 Guillaume Filion, Eduard Valera Zorita and Pol Cusco.
**
** File authors:
** Guillaume Filion (guillaume.filion@gmail.com)
** Eduard Valera Zorita (ezorita@mit.edu)
**
** License:
** 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 3 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, see <http://www.gnu.org/licenses/>.
**
*/

#ifndef _STARCODE_TRIE_PRIVATE_HEADER
#define _STARCODE_TRIE_PRIVATE_HEADER

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109 changes: 57 additions & 52 deletions src/main-starcode.c
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Expand Up @@ -5,8 +5,6 @@
** Guillaume Filion (guillaume.filion@gmail.com)
** Eduard Valera Zorita (ezorita@mit.edu)
**
** Last modified: July 8, 2014
**
** License:
** 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
Expand All @@ -33,14 +31,17 @@

char *USAGE =
"\n"
"Usage:\n"
" starcode\n"
" -v --verbose: verbose\n"
"Usage:"
" starcode [options]\n"
"\n"
" general options:\n"
" -v --version: display version and exit\n"
" -z --verbose: verbose\n"
" -d --dist: maximum Levenshtein distance (default auto)\n"
" -t --threads: number of concurrent threads (default 1)\n"
" -s --sphere: sphere clustering (default message passing)\n"
"\n"
" input/output options (single file)\n"
" input/output options (single file, default)\n"
" -i --input: input file (default stdin)\n"
" -o --output: output file (default stdout)\n"
"\n"
Expand All @@ -49,13 +50,10 @@ char *USAGE =
" -2 --input2: input file 2\n"
"\n"
" output format options\n"
" --non-redundant: remove redundant sequences\n"
"\n"
"By default, the maximum Levenshtein distance depends on the\n"
"length of the sequences. It is equal to 2 + length/30.\n";
" --non-redundant: remove redundant sequences\n";

void say_usage(void) { fprintf(stderr, "%s\n", USAGE); }

void say_version(void) { fprintf(stderr, VERSION "\n"); }
void SIGSEGV_handler(int sig) {
void *array[10];
size_t size;
Expand Down Expand Up @@ -131,7 +129,8 @@ main(
static struct option long_options[] = {
{"non-redundant", no_argument, &nr_flag, 1 },
{"sphere-clustering", no_argument, &sp_flag, 1 },
{"verbose", no_argument, &vb_flag, 1 },
{"version", no_argument, &vb_flag, 'v'},
{"verbose", no_argument, &vb_flag, 'z'},
{"dist", required_argument, 0, 'd'},
{"help", no_argument, 0, 'h'},
{"input", required_argument, 0, 'i'},
Expand All @@ -142,7 +141,7 @@ main(
{0, 0, 0, 0}
};

c = getopt_long(argc, argv, "1:2:d:hi:o:st:v",
c = getopt_long(argc, argv, "1:2:d:hi:o:st:vz",
long_options, &option_index);

// Done parsing options? //
Expand All @@ -158,9 +157,9 @@ main(
input1 = optarg;
}
else {
fprintf(stderr, "--input1 set more than once\n");
fprintf(stderr, "error: --input1 set more than once\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
break;

Expand All @@ -169,30 +168,31 @@ main(
input2 = optarg;
}
else {
fprintf(stderr, "--input2 set more than once\n");
fprintf(stderr, "error: --input2 set more than once\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
break;

case 'd':
if (dist < 0) {
dist = atoi(optarg);
if (dist > STARCODE_MAX_TAU) {
fprintf(stderr, "--dist cannot exceed %d\n",
fprintf(stderr, "error: --dist cannot exceed %d\n",
STARCODE_MAX_TAU);
return 1;
return EXIT_FAILURE;
}
}
else {
fprintf(stderr, "--distance set more than once\n");
fprintf(stderr, "error: --distance set more than once\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
break;

case 'h':
// User asked for help. //
say_version();
say_usage();
return 0;

Expand All @@ -201,9 +201,9 @@ main(
input = optarg;
}
else {
fprintf(stderr, "--input set more than once\n");
fprintf(stderr, "error: --input set more than once\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
break;

Expand All @@ -212,9 +212,9 @@ main(
output = optarg;
}
else {
fprintf(stderr, "--output set more than once\n");
fprintf(stderr, "error: --output set more than once\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
break;

Expand All @@ -227,20 +227,25 @@ main(
threads = atoi(optarg);
}
else {
fprintf(stderr, "--thread set more than once\n");
fprintf(stderr, "error: --thread set more than once\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
break;

case 'v':
case 'z':
vb_flag = 1;
break;

case 'v':
say_version();
return EXIT_SUCCESS;

default:
// Cannot parse. //
say_version();
say_usage();
return 1;
return EXIT_FAILURE;

}

Expand All @@ -255,37 +260,37 @@ main(
else {
fprintf(stderr, "too many options\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
}

// Check options compatibility. //
if (nr_flag && sp_flag) {
fprintf(stderr, "--non-redundant and --spheres are incompatible\n");
fprintf(stderr, "error: --non-redundant and --spheres are incompatible\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
if (input != UNSET && (input1 != UNSET || input2 != UNSET)) {
fprintf(stderr, "--input and --input1/2 are incompatible\n");
fprintf(stderr, "error: --input and --input1/2 are incompatible\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
if (input1 == UNSET && input2 != UNSET) {
fprintf(stderr, "--input1 set without --input2\n");
fprintf(stderr, "error: --input1 set without --input2\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
if (input2 == UNSET && input1 != UNSET) {
fprintf(stderr, "--input2 set without --input1\n");
fprintf(stderr, "error: --input2 set without --input1\n");
say_usage();
return 1;
return EXIT_FAILURE;
}
if (nr_flag && output != UNSET &&
(input1 != UNSET || input2 != UNSET)) {
fprintf(stderr, "cannot specify --output for paired-end "
fprintf(stderr, "error: cannot specify --output for paired-end "
"fastq file with --non-redundant\n");
say_usage();
return 1;
return EXIT_FAILURE;
}

// Set output type. //
Expand All @@ -305,23 +310,23 @@ main(
if (input != UNSET) {
inputf1 = fopen(input, "r");
if (inputf1 == NULL) {
fprintf(stderr, "cannot open file %s\n", input);
fprintf(stderr, "error: cannot open file %s\n", input);
say_usage();
return 1;
return EXIT_FAILURE;
}
}
else if (input1 != UNSET) {
inputf1 = fopen(input1, "r");
if (inputf1 == NULL) {
fprintf(stderr, "cannot open file %s\n", input1);
fprintf(stderr, "error: cannot open file %s\n", input1);
say_usage();
return 1;
return EXIT_FAILURE;
}
inputf2 = fopen(input2, "r");
if (inputf2 == NULL) {
fprintf(stderr, "cannot open file %s\n", input2);
fprintf(stderr, "error: cannot open file %s\n", input2);
say_usage();
return 1;
return EXIT_FAILURE;
}
}
else {
Expand All @@ -331,23 +336,23 @@ main(
if (output != UNSET) {
outputf1 = fopen(output, "w");
if (outputf1 == NULL) {
fprintf(stderr, "cannot write to file %s\n", output);
fprintf(stderr, "error: cannot write to file %s\n", output);
say_usage();
return 1;
return EXIT_FAILURE;
}
}
else if (nr_flag && input1 != UNSET && input2 != UNSET) {
outputf1 = fopen(outname(input1), "w");
if (outputf1 == NULL) {
fprintf(stderr, "cannot write to file %s\n", outname(input1));
fprintf(stderr, "error: cannot write to file %s\n", outname(input1));
say_usage();
return 1;
return EXIT_FAILURE;
}
outputf2 = fopen(outname(input2), "w");
if (outputf2 == NULL) {
fprintf(stderr, "cannot write to file %s\n", outname(input2));
fprintf(stderr, "error: cannot write to file %s\n", outname(input2));
say_usage();
return 1;
return EXIT_FAILURE;
}
}
else {
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2 changes: 0 additions & 2 deletions src/starcode.c
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Expand Up @@ -5,8 +5,6 @@
** Guillaume Filion (guillaume.filion@gmail.com)
** Eduard Valera Zorita (ezorita@mit.edu)
**
** Last modified: October 24, 2014
**
** License:
** 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
Expand Down
2 changes: 1 addition & 1 deletion src/starcode.h
View file
Expand Up @@ -5,7 +5,6 @@
** Guillaume Filion (guillaume.filion@gmail.com)
** Eduard Valera Zorita (ezorita@mit.edu)
**
** Last modified: July 8, 2014
**
** License:
** This program is free software: you can redistribute it and/or modify
Expand All @@ -29,6 +28,7 @@
#define _GNU_SOURCE
#include <stdio.h>

#define VERSION "starcode-v1.0"
#define STARCODE_MAX_TAU 8

typedef enum {
Expand Down
2 changes: 0 additions & 2 deletions src/trie.c
View file
Expand Up @@ -5,8 +5,6 @@
** Guillaume Filion (guillaume.filion@gmail.com)
** Eduard Valera Zorita (ezorita@mit.edu)
**
** Last modified: July 8, 2014
**
** License:
** 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
Expand Down

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