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comparison mrfast-2.1.0.5/CommandLineParser.c @ 1:d4054b05b015 default tip

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Version update to 2.1.0.5
author calkan
date Fri, 09 Mar 2012 07:35:51 -0500
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0:7b3dc85dc7fd 1:d4054b05b015
1 /*
2 * Copyright (c) <2008 - 2012>, 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 names of the University of Washington, Simon Fraser University,
14 * nor the names of its contributors may be
15 * used to endorse or promote products derived from this software without specific
16 * prior written permission.
17 *
18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
28 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30
31 /*
32 Authors:
33 Farhad Hormozdiari
34 Faraz Hach
35 Can Alkan
36 Emails:
37 farhadh AT uw DOT edu
38 fhach AT cs DOT sfu DOT ca
39 calkan AT uw DOT edu
40 */
41
42
43 #include <stdio.h>
44 #include <stdlib.h>
45 #include <getopt.h>
46 #include <string.h>
47 #include <ctype.h>
48 #include "Common.h"
49 #include "CommandLineParser.h"
50
51 int uniqueMode=1;
52 int indexingMode;
53 int searchingMode;
54 int pairedEndMode;
55 int pairedEndDiscordantMode;
56 int transChromosal=0;
57 int pairedEndProfilingMode;
58 int seqCompressed;
59 int outCompressed;
60 int cropSize = 0;
61 int progressRep = 0;
62 int minPairEndedDistance=-1;
63 int maxPairEndedDistance=-1;
64 int minPairEndedDiscordantDistance=-1;
65 int maxPairEndedDiscordantDistance=-1;
66 int bestMode;
67 int nosamMode;
68 char *seqFile1;
69 char *seqFile2;
70 char *mappingOutput = "output";
71 char *mappingOutputPath = "";
72 char *unmappedOutput = "unmapped";
73 char fileName[1000][2][FILE_NAME_LENGTH];
74 int fileCnt;
75 int maxOEAOutput=100;
76 int maxDiscordantOutput=300;
77 unsigned char errThreshold=2;
78 unsigned char maxHits=0;
79 unsigned char WINDOW_SIZE = 12;
80 unsigned int CONTIG_SIZE;
81 unsigned int CONTIG_MAX_SIZE;
82
83 void printHelp();
84
85 int parseCommandLine (int argc, char *argv[])
86 {
87
88 int o;
89 int index;
90 char *fastaFile = NULL;
91 char *batchFile = NULL ;
92 int batchMode = 0;
93
94 static struct option longOptions[] =
95 {
96 {"pe", no_argument, &pairedEndMode, 1},
97 {"discordant-vh", no_argument, &pairedEndDiscordantMode, 1},
98 {"trans", no_argument, &transChromosal , 1},
99 {"profile", no_argument, &pairedEndProfilingMode, 1},
100 {"seqcomp", no_argument, &seqCompressed, 1},
101 {"outcomp", no_argument, &outCompressed, 1},
102 {"progress", no_argument, &progressRep, 1},
103 {"best", no_argument, &bestMode, 1},
104 {"index", required_argument, 0, 'i'},
105 {"search", required_argument, 0, 's'},
106 {"help", no_argument, 0, 'h'},
107 {"version", no_argument, 0, 'v'},
108 {"seq", required_argument, 0, 'x'},
109 {"seq1", required_argument, 0, 'x'},
110 {"seq2", required_argument, 0, 'y'},
111 {"ws", required_argument, 0, 'w'},
112 {"min", required_argument, 0, 'l'},
113 {"max", required_argument, 0, 'm'},
114 {"crop", required_argument, 0, 'c'},
115 {"maxoea", required_argument, 0, 'a'},
116 {"maxdis", required_argument, 0, 'd'},
117 {"nosam", no_argument, &nosamMode, 1},
118 {0, 0, 0, 0},
119 };
120
121 while ( (o = getopt_long ( argc, argv, "bhvn:e:o:u:i:s:x:y:w:l:m:c:a:d:", longOptions, &index)) != -1 )
122 {
123 switch (o)
124 {
125 case 'a':
126 maxOEAOutput = atoi(optarg);
127 if (maxOEAOutput == 0)
128 maxOEAOutput = 100000;
129 break;
130 case 'd':
131 maxDiscordantOutput = atoi(optarg);
132 if (maxDiscordantOutput == 0)
133 maxDiscordantOutput = 100000;
134 break;
135 case 'i':
136 indexingMode = 1;
137 fastaFile = optarg;
138 break;
139 case 's':
140 searchingMode = 1;
141 fastaFile = optarg;
142 break;
143 case 'b':
144 batchMode = 1;
145 break;
146 case 'c':
147 cropSize = atoi(optarg);
148 break;
149 case 'w':
150 WINDOW_SIZE = atoi(optarg);
151 break;
152 case 'x':
153 seqFile1 = optarg;
154 break;
155 case 'y':
156 seqFile2 = optarg;
157 break;
158 case 'u':
159 unmappedOutput = optarg;
160 break;
161 case 'o':
162 mappingOutput = getMem(FILE_NAME_LENGTH);
163 mappingOutputPath = getMem(FILE_NAME_LENGTH);
164 stripPath (optarg, &mappingOutputPath, &mappingOutput);
165 break;
166 case 'n':
167 maxHits = atoi(optarg);
168 break;
169 case 'e':
170 errThreshold = atoi(optarg);
171 break;
172 case 'l':
173 minPairEndedDistance = atoi(optarg);
174 break;
175 case 'm':
176 maxPairEndedDistance = atoi(optarg);
177 break;
178 case 'h':
179 printHelp();
180 return 0;
181 break;
182 case 'v':
183 fprintf(stdout, "%s.%s\n", versionNumber, versionNumberF);
184 return 0;
185 break;
186 /* case '?':
187 fprintf(stderr, "Unknown parameter: %s\n", longOptions[index].name);
188 abort();
189 break;*/
190 }
191
192 }
193 if (indexingMode + searchingMode != 1)
194 {
195 fprintf(stdout, "ERROR: Indexing / Searching mode should be selected\n");
196 return 0;
197 }
198
199 if (WINDOW_SIZE > 15 || WINDOW_SIZE < 11)
200 {
201 fprintf(stdout, "ERROR: Window size should be in [12..15]\n");
202 return 0;
203 }
204
205
206 if ( indexingMode )
207 {
208 CONTIG_SIZE = 15000000;
209 CONTIG_MAX_SIZE = 40000000;
210
211 if (batchMode)
212 {
213 batchFile = fastaFile;
214 fastaFile = NULL;
215 }
216
217 if (batchFile == NULL && fastaFile == NULL)
218 {
219 fprintf(stdout, "ERROR: Reference(s) should be indicated for indexing\n");
220 return 0;
221 }
222
223 if (pairedEndDiscordantMode)
224 {
225 fprintf(stdout, "ERROR: --discordant-vh cannot be used in indexing mode. \n");
226 return 0;
227 }
228
229 }
230
231
232 if ( searchingMode )
233 {
234 CONTIG_SIZE = 300000000;
235 CONTIG_MAX_SIZE = 300000000;
236
237
238 if (batchMode)
239 {
240 batchFile = fastaFile;
241 fastaFile = NULL;
242 }
243
244 if (batchFile == NULL && fastaFile == NULL)
245 {
246 fprintf(stdout, "ERROR: Index File(s) should be indiciated for searching\n");
247 return 0;
248 }
249
250 if (seqFile1 == NULL && seqFile2 == NULL)
251 {
252 fprintf(stdout, "ERROR: Please indicate a sequence file for searching.\n");
253 return 0;
254 }
255
256
257 if (!pairedEndMode && seqFile2 != NULL)
258 {
259 fprintf(stdout, "ERROR: Second File can be indicated in pairedend mode\n");
260 return 0;
261 }
262
263 if (pairedEndMode && (minPairEndedDistance <0 || maxPairEndedDistance < 0 || minPairEndedDistance > maxPairEndedDistance))
264 {
265 fprintf(stdout, "ERROR: Please enter a valid range for pairedend sequences.\n");
266 return 0;
267 }
268
269 if (pairedEndMode && seqFile1 == NULL)
270 {
271 fprintf(stdout, "ERROR: Please indicate the first file for pairedend search.\n");
272 return 0;
273 }
274
275 if (!pairedEndMode && pairedEndDiscordantMode)
276 {
277 fprintf(stdout, "ERROR: --discordant should be used with --pe");
278 return 0;
279 }
280
281 if (!pairedEndMode && pairedEndProfilingMode)
282 {
283 fprintf(stdout, "ERROR: --profile should be used with --pe");
284 return 0;
285 }
286
287 if (pairedEndMode)
288 pairedEndDiscordantMode = 1;
289 }
290
291 int i = 0;
292
293
294 if (batchMode)
295 {
296 FILE *fp = fileOpen(batchFile, "r");
297
298 if (fp == NULL)
299 return 0;
300
301 fileCnt = 0;
302
303 while ( fgets(fileName[fileCnt][0], FILE_NAME_LENGTH, fp))
304 {
305 for (i = strlen(fileName[fileCnt][0])-1; i>=0; i--)
306 if ( !isspace(fileName[fileCnt][0][i]))
307 break;
308 fileName[fileCnt][0][i+1] = '\0';
309
310 if (strcmp(fileName[fileCnt][0], "") != 0)
311 {
312 sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]);
313 fileCnt++;
314 }
315 }
316 }
317 else
318 {
319 sprintf(fileName[fileCnt][0], "%s", fastaFile);
320 sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]);
321 fileCnt++;
322 }
323
324
325 if (pairedEndProfilingMode)
326 {
327
328 minPairEndedDistance = 0;
329 maxPairEndedDistance = 300000000;
330
331 }
332
333 if (pairedEndDiscordantMode)
334 {
335 minPairEndedDiscordantDistance = minPairEndedDistance;
336 maxPairEndedDiscordantDistance = maxPairEndedDistance;
337
338 minPairEndedDistance = 0;
339 maxPairEndedDistance = 300000000;
340 }
341
342 return 1;
343 }
344
345
346 void printHelp()
347 {
348 char *errorType;
349 if (mrFAST)
350 {
351 fprintf(stdout,"mrFAST : Micro-Read Fast Alignment Search Tool.\n\n");
352 fprintf(stdout,"Usage: mrfast [options]\n\n");
353 errorType="edit distance";
354 }
355 else
356 {
357 fprintf(stdout,"mrsFAST : Micro-Read Substitutions (only) Fast Alignment Search Tool.\n\n");
358 fprintf(stdout,"mrsFAST is a cache oblivious read mapping tool. mrsFAST capable of mapping\n");
359 fprintf(stdout,"single and paired end reads to the reference genome. Bisulfite treated \n");
360 fprintf(stdout,"sequences are not supported in this version. By default mrsFAST reports \n");
361 fprintf(stdout,"the output in SAM format.\n\n");
362 fprintf(stdout,"Usage: mrsFAST [options]\n\n");
363 errorType="hamming distance";
364 }
365
366 fprintf(stdout,"General Options:\n");
367 fprintf(stdout," -v|--version\t\tCurrent Version.\n");
368 fprintf(stdout," -h\t\t\tShows the help file.\n");
369 fprintf(stdout,"\n\n");
370
371 fprintf(stdout,"Indexing Options:\n");
372 fprintf(stdout," --index [file]\t\tGenerate an index from the specified fasta file. \n");
373 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");
374 fprintf(stdout," --ws [int]\t\tSet window size for indexing (default:12 max:14).\n");
375 fprintf(stdout,"\n\n");
376
377 fprintf(stdout,"Searching Options:\n");
378 fprintf(stdout," --search [file]\tSearch in the specified genome. Provide the path to the fasta file. \n\t\t\tIndex file should be in the same directory.\n");
379 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");
380 fprintf(stdout," --pe \t\t\tSearch will be done in Paired-End mode.\n");
381 fprintf(stdout," --seq [file]\t\tInput sequences in fasta/fastq format [file]. If \n\t\t\tpaired end reads are interleaved, use this option.\n");
382 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\tpaired end reads. \n");
383 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\tpaired end reads. \n");
384 fprintf(stdout," -o [file]\t\tOutput of the mapped sequences. The default is \"output\".\n");
385 fprintf(stdout," -u [file]\t\tSave unmapped sequences in fasta/fastq format.\n");
386 fprintf(stdout," --best \t\tOnly the best mapping from all the possible mapping is returned.\n");
387 fprintf(stdout," --seqcomp \t\tIndicates that the input sequences are compressed (gz).\n");
388 fprintf(stdout," --outcomp \t\tIndicates that output file should be compressed (gz).\n");
389 fprintf(stdout," -e [int]\t\tMaximum allowed %s (default 2).\n", errorType);
390 fprintf(stdout," --min [int]\t\tMin distance allowed between a pair of end sequences.\n");
391 fprintf(stdout," --max [int]\t\tMax distance allowed between a pair of end sequences.\n");
392
393 fprintf(stdout," --maxoea [int]\t\tMax number of One End Anchored (OEA) returned for each read pair. We recommend 100 or above for NovelSeq use.\n");
394 fprintf(stdout," --maxdis [int]\t\tMax number of discordant map locations returned for each read pair. We recommend 300 or above for VariationHunter use.\n");
395 }