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comparison mrsfast-2.3.0.2/CommandLineParser.c @ 0:ec628ba33878 default tip

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Uploaded source code for mrsFAST
author calkan
date Tue, 21 Feb 2012 10:39:28 -0500
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-1:000000000000 0:ec628ba33878
1 /*
2 * Copyright (c) <2008 - 2009>, University of Washington, Simon Fraser University
3 * All rights reserved.
4 *
5 * Redistribution and use in source and binary forms, with or without modification,
6 * are permitted provided that the following conditions are met:
7 *
8 * Redistributions of source code must retain the above copyright notice, this list
9 * of conditions and the following disclaimer.
10 * - Redistributions in binary form must reproduce the above copyright notice, this
11 * list of conditions and the following disclaimer in the documentation and/or other
12 * materials provided with the distribution.
13 * - Neither the name of the <ORGANIZATION> nor the names of its contributors may be
14 * used to endorse or promote products derived from this software without specific
15 * prior written permission.
16 *
17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
28 */
29
30 /*
31 * Author : Faraz Hach
32 * Email : fhach AT cs DOT sfu
33 * Last Update : 2009-01-29
34 */
35
36 #include <stdio.h>
37 #include <stdlib.h>
38 #include <getopt.h>
39 #include <string.h>
40 #include <ctype.h>
41 #include "Common.h"
42 #include "CommandLineParser.h"
43
44 int uniqueMode=1;
45 int indexingMode;
46 int searchingMode;
47 int bisulfiteMode;
48 int pairedEndMode;
49 int pairedEndDiscordantMode;
50 int pairedEndProfilingMode;
51 int seqCompressed;
52 int outCompressed;
53 int cropSize = 0;
54 int progressRep = 0;
55 int minPairEndedDistance=-1;
56 int maxPairEndedDistance=-1;
57 int minPairEndedDiscordantDistance=-1;
58 int maxPairEndedDiscordantDistance=-1;
59 char *seqFile1;
60 char *seqFile2;
61 char *mappingOutput = "output";
62 char *mappingOutputPath = "";
63 char *unmappedOutput = "";
64 char fileName[1000][2][FILE_NAME_LENGTH];
65 int fileCnt;
66 unsigned char errThreshold=2;
67 unsigned char maxHits=0;
68 unsigned char WINDOW_SIZE = 12;
69 unsigned int CONTIG_SIZE;
70 unsigned int CONTIG_MAX_SIZE;
71
72 void printHelp();
73
74 int parseCommandLine (int argc, char *argv[])
75 {
76
77 int o;
78 int index;
79 char *fastaFile = NULL;
80 char *fastaOutputFile = NULL;
81 char *indexFile = NULL;
82 char *batchFile = NULL ;
83 int batchMode = 0;
84 static struct option longOptions[] =
85 {
86
87 // {"bs", no_argument, &bisulfiteMode, 1},
88 {"pe", no_argument, &pairedEndMode, 1},
89 {"discordant-vh", no_argument, &pairedEndDiscordantMode, 1},
90 {"profile", no_argument, &pairedEndProfilingMode, 1},
91 {"seqcomp", no_argument, &seqCompressed, 1},
92 {"outcomp", no_argument, &outCompressed, 1},
93 {"progress", no_argument, &progressRep, 1},
94 {"index", required_argument, 0, 'i'},
95 {"search", required_argument, 0, 's'},
96 {"help", no_argument, 0, 'h'},
97 {"version", no_argument, 0, 'v'},
98 {"seq", required_argument, 0, 'x'},
99 {"seq1", required_argument, 0, 'x'},
100 {"seq2", required_argument, 0, 'y'},
101 {"ws", required_argument, 0, 'w'},
102 {"min", required_argument, 0, 'l'},
103 {"max", required_argument, 0, 'm'},
104 {"crop", required_argument, 0, 'c'}
105
106 };
107
108
109
110 while ( (o = getopt_long ( argc, argv, "f:i:u:o:s:e:n:bhv", longOptions, &index))!= -1 )
111 {
112 switch (o)
113 {
114 case 'i':
115 indexingMode = 1;
116 fastaFile = optarg;
117 break;
118 case 's':
119 searchingMode = 1;
120 fastaFile = optarg;
121 break;
122 case 'b':
123 batchMode = 1;
124 break;
125 case 'c':
126 cropSize = atoi(optarg);
127 break;
128 case 'w':
129 WINDOW_SIZE = atoi(optarg);
130 break;
131 case 'x':
132 seqFile1 = optarg;
133 break;
134 case 'y':
135 seqFile2 = optarg;
136 break;
137 case 'u':
138 unmappedOutput = optarg;
139 break;
140 case 'o':
141 mappingOutput = getMem(FILE_NAME_LENGTH);
142 mappingOutputPath = getMem(FILE_NAME_LENGTH);
143 stripPath (optarg, &mappingOutputPath, &mappingOutput);
144 break;
145 case 'n':
146 maxHits = atoi(optarg);
147 break;
148 case 'e':
149 errThreshold = atoi(optarg);
150 break;
151 case 'l':
152 minPairEndedDistance = atoi(optarg);
153 break;
154 case 'm':
155 maxPairEndedDistance = atoi(optarg);
156 break;
157 case 'h':
158 printHelp();
159 return 0;
160 break;
161 case 'v':
162 fprintf(stdout, "%s.%s\n", versionNumber, versionNumberF);
163 return 0;
164 break;
165 }
166
167 }
168
169 if (indexingMode + searchingMode != 1)
170 {
171 fprintf(stdout, "ERROR: Indexing / Searching mode should be selected\n");
172 return 0;
173 }
174
175 if (WINDOW_SIZE > 14 || WINDOW_SIZE < 8)
176 {
177 fprintf(stdout, "ERROR: Window size should be in [8..14]\n");
178 return 0;
179 }
180
181
182 if ( indexingMode )
183 {
184 CONTIG_SIZE = 15000000;
185 CONTIG_MAX_SIZE = 40000000;
186
187 if (batchMode)
188 {
189 batchFile = fastaFile;
190 fastaFile = NULL;
191 }
192
193 if (batchFile == NULL && fastaFile == NULL)
194 {
195 fprintf(stdout, "ERROR: Reference(s) should be indicated for indexing\n");
196 return 0;
197 }
198
199 if (pairedEndDiscordantMode)
200 {
201 fprintf(stdout, "ERROR: --discordant cannot be used in indexing mode. \n");
202 return 0;
203 }
204
205 }
206
207
208 if ( searchingMode )
209 {
210 CONTIG_SIZE = 300000000;
211 CONTIG_MAX_SIZE = 300000000;
212
213
214 if (batchMode)
215 {
216 batchFile = fastaFile;
217 fastaFile = NULL;
218 }
219
220 if (batchFile == NULL && fastaFile == NULL)
221 {
222 fprintf(stdout, "ERROR: Index File(s) should be indiciated for searching\n");
223 return 0;
224 }
225
226 if (seqFile1 == NULL && seqFile2 == NULL)
227 {
228 fprintf(stdout, "ERROR: Please indicate a sequence file for searching.\n");
229 return 0;
230 }
231
232
233 if (!pairedEndMode && !bisulfiteMode && seqFile2 != NULL)
234 {
235 fprintf(stdout, "ERROR: Second File can be indicated in pairedend/bisulfite mode\n");
236 return 0;
237 }
238
239 if (pairedEndMode && (minPairEndedDistance <0 || maxPairEndedDistance < 0 || minPairEndedDistance > maxPairEndedDistance))
240 {
241 fprintf(stdout, "ERROR: Please enter a valid range for pairedend sequences.\n");
242 return 0;
243 }
244
245 if (pairedEndMode && seqFile1 == NULL)
246 {
247 fprintf(stdout, "ERROR: Please indicate the first file for pairedend search.\n");
248 return 0;
249 }
250
251 if (!pairedEndMode && pairedEndDiscordantMode)
252 {
253 fprintf(stdout, "ERROR: --discordant should be used with --pe");
254 return 0;
255 }
256
257 if (!pairedEndMode && pairedEndProfilingMode)
258 {
259 fprintf(stdout, "ERROR: --profile should be used with --pe");
260 return 0;
261 }
262 }
263
264 int i = 0;
265
266
267 if (batchMode)
268 {
269 FILE *fp = fileOpen(batchFile, "r");
270
271 if (fp == NULL)
272 return 0;
273
274 fileCnt = 0;
275
276 while ( fgets(fileName[fileCnt][0], FILE_NAME_LENGTH, fp))
277 {
278 for (i = strlen(fileName[fileCnt][0])-1; i>=0; i--)
279 if ( !isspace(fileName[fileCnt][0][i]))
280 break;
281 fileName[fileCnt][0][i+1] = '\0';
282
283 if (strcmp(fileName[fileCnt][0], "") != 0)
284 {
285 if (bisulfiteMode)
286 sprintf(fileName[fileCnt][1], "%s.bsindex", fileName[fileCnt][0]);
287 else
288 sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]);
289 fileCnt++;
290 }
291 }
292 }
293 else
294 {
295 sprintf(fileName[fileCnt][0], "%s", fastaFile);
296 if (bisulfiteMode)
297 sprintf(fileName[fileCnt][1], "%s.bsindex", fileName[fileCnt][0]);
298 else
299 sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]);
300 fileCnt++;
301 }
302
303
304 if (pairedEndProfilingMode)
305 {
306
307 minPairEndedDistance = 0;
308 maxPairEndedDistance = 300000000;
309
310 }
311
312 if (pairedEndDiscordantMode)
313 {
314 minPairEndedDiscordantDistance = minPairEndedDistance;
315 maxPairEndedDiscordantDistance = maxPairEndedDistance;
316
317 minPairEndedDistance = 0;
318 maxPairEndedDistance = 300000000;
319 }
320
321 return 1;
322 }
323
324
325 void printHelp()
326 {
327 char *errorType;
328 if (mrFAST)
329 {
330 fprintf(stdout,"mrFAST : Micro-Read Fast Alignment Search Tool.\n\n");
331 fprintf(stdout,"Usage: mrFAST [options]\n\n");
332 errorType="edit distance";
333 }
334 else
335 {
336 fprintf(stdout,"mrsFAST : Micro-Read Substitutions (only) Fast Alignment Search Tool.\n\n");
337 fprintf(stdout,"mrsFAST is a cache oblivious read mapping tool. mrsFAST capable of mapping\n");
338 fprintf(stdout,"single and paired end reads to the reference genome. Bisulfite treated \n");
339 fprintf(stdout,"sequences are not supported in this version. By default mrsFAST reports \n");
340 fprintf(stdout,"the output in SAM format.\n\n");
341 fprintf(stdout,"Usage: mrsFAST [options]\n\n");
342 errorType="hamming distance";
343 }
344
345 fprintf(stdout,"General Options:\n");
346 fprintf(stdout," -v|--version\t\tCurrent Version.\n");
347 fprintf(stdout," -h\t\t\tShows the help file.\n");
348 fprintf(stdout,"\n\n");
349
350 fprintf(stdout,"Indexing Options:\n");
351 fprintf(stdout," --index [file]\t\tGenerate an index from the specified fasta file. \n");
352 fprintf(stdout," -b\t\t\tIndicates the indexing will be done in batch mode.\n\t\t\tThe file specified in --index should contain the \n\t\t\tlist of fasta files.\n");
353 fprintf(stdout," -ws [int]\t\tSet window size for indexing (default:12-min:8 max:14).\n");
354 // fprintf(stdout," -bs \t\t\tBisulfite mode.");
355 fprintf(stdout,"\n\n");
356
357 fprintf(stdout,"Searching Options:\n");
358 fprintf(stdout," --search [file]\tSearch the specified genome. Index file should be \n\t\t\tin same directory as the fasta file.\n");
359 fprintf(stdout," -b\t\t\tIndicates the mapping will be done in batch mode. \n\t\t\tThe file specified in --search should contain the \n\t\t\tlist of fasta files.\n");
360 fprintf(stdout," --pe \t\t\tSearch will be done in Pairedend mode.\n");
361 // fprintf(stdout," --bs \t\t\tSearch will be done in Bisulfite mode.\n");
362 fprintf(stdout," --seq [file]\t\tInput sequences in fasta/fastq format [file]. If \n\t\t\tpairend reads are interleaved, use this option.\n");
363 fprintf(stdout," --seq1 [file]\t\tInput sequences in fasta/fastq format [file] (First \n\t\t\tfile). Use this option to indicate the first file of \n\t\t\tpair-end reads. You can use this option alone in \n\t\t\tbisulfite mode. \n");
364 fprintf(stdout," --seq2 [file]\t\tInput sequences in fasta/fastq format [file] (Second \n\t\t\tfile). Use this option to indicate the second file of \n\t\t\tpair-end reads. You can use this option alone in \n\t\t\tbisulfite mode. \n");
365 fprintf(stdout," -o [file]\t\tOutput of the mapped sequences. The default is output.\n");
366 fprintf(stdout," --seqcomp \t\tIndicates that the input sequences are compressed(gz).\n");
367 fprintf(stdout," --outcomp \t\tIndicates that output file should be compressed(gz).\n");
368 // fprintf(stdout," -u [file]\t\tSave unmapped sequences to the [file] in fasta format.\n");
369 fprintf(stdout," -n [int]\t\tMaximum number of locations reported for a sequence \n\t\t\t(default 0, all mappings). \n");
370 fprintf(stdout," -e [int]\t\t%s (default 2).\n", errorType);
371 fprintf(stdout," --min [int]\t\tMin inferred distance allowed between two pairend sequences.\n");
372 fprintf(stdout," --max [int]\t\tMax inferred distance allowed between two pairend sequences.\n");
373 }