CommandLineParser.c

/*
 * Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, 
 * Bilkent University and Carnegie Mellon University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without modification,
 * are permitted provided that the following conditions are met:
 *
 * Redistributions of source code must retain the above copyright notice, this list
 * of conditions and the following disclaimer.
 * - Redistributions in binary form must reproduce the above copyright notice, this
 *   list of conditions and the following disclaimer in the documentation and/or other
 *   materials provided with the distribution.
 * - Neither the names of the University of Washington, Simon Fraser University, 
 *   Bilkent University, Carnegie Mellon University,
 *   nor the names of its contributors may be
 *   used to endorse or promote products derived from this software without specific
 *   prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

  Authors: 
  Farhad Hormozdiari
	  farhadh AT uw DOT edu
  Faraz Hach
	  fhach AT cs DOT sfu DOT ca
  Can Alkan
	  calkan AT gmail DOT com
  Hongyi Xin
	  gohongyi AT gmail DOT com
  Donghyuk Lee
	  bleups AT gmail DOT com
*/



#include <stdio.h>
#include <stdlib.h>
#include <getopt.h>
#include <string.h>
#include <ctype.h>
#include "Common.h"
#include "CommandLineParser.h"

int				uniqueMode=1;
int				indexingMode;
int				searchingMode;
int				pairedEndMode;
int				pairedEndModeMP;
int				pairedEndModePE;
int				pairedEndDiscordantMode;
int				transChromosomal=0;
int				pairedEndProfilingMode;
int				seqCompressed;
int				outCompressed;
int				cropSize = 0;
int				progressRep = 0;
int				minPairEndedDistance=-1;
int				maxPairEndedDistance=-1;
int				minPairEndedDiscordantDistance=-1;
int				maxPairEndedDiscordantDistance=-1;
int 				bestMode;
int 				nosamMode;
int                             debugMode=0;
char				*seqFile1;
char				*seqFile2;
char				*mappingOutput = "output";
char				*mappingOutputPath = "";
char				*unmappedOutput = "unmapped";
char				fileName[2][FILE_NAME_LENGTH];
int 				maxOEAOutput=100;
int 				maxDiscordantOutput=300;
unsigned char			errThreshold=255;
unsigned char			maxHits=0;
unsigned char			WINDOW_SIZE = 12;
unsigned int			CONTIG_SIZE;
unsigned int			CONTIG_MAX_SIZE;
char                            readGroup[FILE_NAME_LENGTH];
char                            sampleName[FILE_NAME_LENGTH];
char                            libName[FILE_NAME_LENGTH];

void printHelp();

int parseCommandLine (int argc, char *argv[])
{
  
  int o;
  int index;
  char *fastaFile = NULL;

  readGroup[0] = 0;
  sampleName[0] = 0;
  libName[0] = 0;
  
  static struct option longOptions[] = 
    {
      {"mp",   	        no_argument,	    &pairedEndModeMP,		1},
      {"pe",		no_argument,  	    &pairedEndModePE,		1},
      {"discordant-vh", no_argument,	    &pairedEndDiscordantMode,	1},
      {"trans",         no_argument,        &transChromosomal,          1},
      {"profile",       no_argument, 	    &pairedEndProfilingMode,	1},
      {"seqcomp",	no_argument,	    &seqCompressed,		1},
      {"outcomp",       no_argument,	    &outCompressed,		1},
      {"progress",	no_argument,	    &progressRep,		1},
      {"best",		no_argument,	    &bestMode,		1},
      {"debug",		no_argument,	    &debugMode,		1},
      {"index",		required_argument,  0, 			'i'},
      {"search",	required_argument,  0,			's'},
      {"help",		no_argument,	    0,			'h'},
      {"version",	no_argument,	    0,			'v'},
      {"quiet",	        no_argument,	    0,			'q'},
      {"seq",		required_argument,  0,			'x'},
      {"seq1",		required_argument,  0,			'x'},
      {"seq2",		required_argument,  0,			'y'},
      {"ws",		required_argument,  0,			'w'},
      {"min",		required_argument,  0,			'l'},
      {"max",		required_argument,  0,			'm'},
      {"crop",		required_argument,  0,			'c'},
      {"maxoea",        required_argument,  0,                  'a'},
      {"maxdis",        required_argument,  0,                  'd'},
      {"rg",            required_argument,  0,                  'g'},
      {"sample",        required_argument,  0,                  'p'},
      {"lib",           required_argument,  0,                  'r'},
      {"nosam",         no_argument,        &nosamMode,         1},
      {0,  0,  0, 0},
    };

  if (argc == 1){
    printHelp();
    return 0;
  }

  while ( (o = getopt_long ( argc, argv, "hvn:e:o:u:i:s:x:y:w:l:m:c:a:d:g:p:r:", longOptions, &index)) != -1 )
    {
      switch (o)
	{
	case 'a':
	  maxOEAOutput = atoi(optarg);
	  if (maxOEAOutput == 0)
	    maxOEAOutput = 100000;
	  break;
	case 'd':
	  maxDiscordantOutput = atoi(optarg);
	  if (maxDiscordantOutput == 0)
	    maxDiscordantOutput = 100000;
	  break;
	case 'i':
	  indexingMode = 1;
	  fastaFile = optarg;
	  break;
	case 's':
	  searchingMode = 1;
	  fastaFile = optarg;
	  break;
	case 'c': 
	  cropSize = atoi(optarg);
	  break;
	case 'w':
	  WINDOW_SIZE = atoi(optarg);
	  break;
	case 'x':
	  seqFile1 = optarg;
	  break;
	case 'y':
	  seqFile2 = optarg;
	  break;
	case 'u':
	  unmappedOutput = optarg;
	  break;
	case 'o':
	  mappingOutput = getMem(FILE_NAME_LENGTH);
	  mappingOutputPath = getMem(FILE_NAME_LENGTH);
	  stripPath (optarg, &mappingOutputPath, &mappingOutput);
	  break;
	case 'n':
	  maxHits = atoi(optarg);
	  break;
	case 'e':
	  errThreshold = atoi(optarg);
	  break;
	case 'l':
	  minPairEndedDistance = atoi(optarg);
	  break;
	case 'm':
	  maxPairEndedDistance = atoi(optarg);
	  break;					
	case 'g':
	  strcpy(readGroup, optarg);
	  break;					
	case 'p':
	  strcpy(sampleName, optarg);
	  break;					
	case 'r':
	  strcpy(libName, optarg);
	  break;					
	case 'h':
	  printHelp();
	  return 0;
	  break;
	case 'v':
	  fprintf(stderr, "mrFAST %s.%s with FastHASH\n", versionNumber, versionNumberF);
	  return 0;
	  break;				
	case 'q':
	  if (freopen("/dev/null", "w", stderr) == NULL)
	    fprintf(stderr, "Quiet mode failure.\n");
	  break;				
	case '?': 
	  fprintf(stderr, "Unknown parameter: %s\n", longOptions[index].name);
	  abort();
	  return 0;
	  break;
	}

    }
  
  if (indexingMode + searchingMode != 1)
    {
      fprintf(stderr, "ERROR: Indexing / Searching mode should be selected\n");
      return 0;
    }

  if (WINDOW_SIZE > 15 || WINDOW_SIZE < 11)
    {
      fprintf(stderr, "ERROR: Window size should be in [12..15]\n");
      return 0;
    }


  if ( indexingMode )
    {
      CONTIG_SIZE	= 120000000;
      CONTIG_MAX_SIZE	= 250000000;

      if (fastaFile == NULL)
	{
	  fprintf(stderr, "ERROR: Reference(s) should be indicated for indexing\n");
	  return 0;
	}

      if (pairedEndDiscordantMode)
	{
	  fprintf(stderr, "ERROR: --discordant-vh cannot be used in indexing mode. \n");
	  return 0;
	}

    }


  if ( searchingMode )
    {
      CONTIG_SIZE	= 330000000;
      CONTIG_MAX_SIZE	= 330000000;
      
      if (pairedEndModeMP && pairedEndModePE){
	fprintf(stderr, "ERROR: Use either --pe or --mp, not both. \n");
	return 0;
      }
      
      pairedEndMode = (pairedEndModeMP || pairedEndModePE);
		
      if (fastaFile == NULL)
	{
	  fprintf(stderr, "ERROR: Index File should be indiciated for searching\n");
	  return 0;
	}

      if (seqFile1 == NULL && seqFile2 == NULL)
	{
	  fprintf(stderr, "ERROR: Please indicate a sequence file for searching.\n");
	  return 0;
	}


      if (!pairedEndMode && seqFile2 != NULL)
	{
	  fprintf(stderr, "ERROR: Second File can be indicated in pairedend mode\n");
	  return 0;
	}

      if (pairedEndMode && (minPairEndedDistance <0 || maxPairEndedDistance < 0 || minPairEndedDistance > maxPairEndedDistance))
	{
	  fprintf(stderr, "ERROR: Please enter a valid range for pairedend sequences.\n");
	  return 0;
	}

      if (pairedEndMode && seqFile1 == NULL)
	{
	  fprintf(stderr, "ERROR: Please indicate the first file for pairedend search.\n");
	  return 0;
	}

      if (!pairedEndMode && pairedEndDiscordantMode)
	{
	  fprintf(stderr, "ERROR: --discordant-vh should be used with --pe\n");
	  return 0;
	}

      if (!pairedEndMode && pairedEndProfilingMode)
	{
	  fprintf(stderr, "ERROR: --profile should be used with --pe\n");
	  return 0;
	}

      if (pairedEndMode)
	pairedEndDiscordantMode = 1;
		
      if (readGroup[0] != 0 && sampleName[0] == 0)
	{
	  fprintf(stderr, "ERROR: --sample should be used with --rg\n");
	  return 0;
	}

      if (readGroup[0] != 0 && libName[0] == 0)
	{
	  fprintf(stderr, "ERROR: --lib should be used with --rg\n");
	  return 0;
	}

      if (readGroup[0] == 0 && sampleName[0] != 0)
	{
	  fprintf(stderr, "ERROR: --rg should be used with --sample\n");
	  return 0;
	}

      if (readGroup[0] == 0 && libName[0] != 0)
	{
	  fprintf(stderr, "ERROR: --rg should be used with --lib\n");
	  return 0;
	}

    }

  sprintf(fileName[0], "%s", fastaFile);
  sprintf(fileName[1], "%s.index", fileName[0]); 
       


  if (pairedEndProfilingMode)
    {

      minPairEndedDistance = 0;
      maxPairEndedDistance = 300000000;

    }

  if (pairedEndDiscordantMode)
    {
      minPairEndedDiscordantDistance = minPairEndedDistance;
      maxPairEndedDiscordantDistance = maxPairEndedDistance;

      minPairEndedDistance = 0;
      maxPairEndedDistance = 300000000;
    }
  
  return 1;
}


void printHelp()
{
  char *errorType;
  if (mrFAST)
    {
      fprintf(stderr,"mrFAST : Micro-Read Fast Alignment Search Tool. Enhanced with FastHASH.\n\n");
      fprintf(stderr,"Usage: mrfast [options]\n\n");
      errorType="edit distance";
    }
  else
    {
      fprintf(stderr,"mrsFAST : Micro-Read Substitutions (only) Fast Alignment Search Tool.\n\n");
      fprintf(stderr,"mrsFAST is a cache oblivious read mapping tool. mrsFAST capable of mapping\n");
      fprintf(stderr,"single and paired end reads to the reference genome. Bisulfite treated \n");
      fprintf(stderr,"sequences are not supported in this version. By default mrsFAST reports  \n");
      fprintf(stderr,"the output in SAM format.\n\n");
      fprintf(stderr,"Usage: mrsFAST [options]\n\n");
      errorType="hamming distance";
    }

  fprintf(stderr,"General Options:\n");
  fprintf(stderr," -v|--version\t\tCurrent Version.\n");
  fprintf(stderr," -h\t\t\tShows the help file.\n");
  fprintf(stderr,"\n\n");

  fprintf(stderr,"Indexing Options:\n");
  fprintf(stderr," --index [file]\t\tGenerate an index from the specified fasta file. \n");
  fprintf(stderr," --ws [int]\t\tSet window size for indexing (default:12 max:14).\n");
  fprintf(stderr,"\n\n");

  fprintf(stderr,"Searching Options:\n");
  fprintf(stderr," --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");
  fprintf(stderr," --pe \t\t\tSearch will be done in Paired-End mode.\n");
  fprintf(stderr," --seq [file]\t\tInput sequences in fasta/fastq format [file]. If \n\t\t\tpaired end reads are interleaved, use this option.\n");
  fprintf(stderr," --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");
  fprintf(stderr," --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");
  fprintf(stderr," -o [file]\t\tOutput of the mapped sequences. The default is \"output\".\n");
  fprintf(stderr," -u [file]\t\tSave unmapped sequences in fasta/fastq format.\n");
  fprintf(stderr," --best   \t\tOnly the best mapping from all the possible mapping is returned.\n");
  fprintf(stderr," --seqcomp \t\tIndicates that the input sequences are compressed (gz).\n");
  fprintf(stderr," --outcomp \t\tIndicates that output file should be compressed (gz).\n");
  fprintf(stderr," -e [int]\t\tMaximum allowed %s (default 4%% of the read length).\n", errorType);
  fprintf(stderr," --min [int]\t\tMin distance allowed between a pair of end sequences.\n");
  fprintf(stderr," --max [int]\t\tMax distance allowed between a pair of end sequences.\n");
  fprintf(stderr," --maxoea [int]\t\tMax number of One End Anchored (OEA) returned for each read pair.\n\t\t\tWe recommend 100 or above for NovelSeq use. Default = 100.\n");
  fprintf(stderr," --maxdis [int]\t\tMax number of discordant map locations returned for each read pair.\n\t\t\tWe recommend 300 or above for VariationHunter use. Default = 300.\n");
  fprintf(stderr," --crop [int]\t\tTrim the reads to the given length.\n");
  fprintf(stderr," --sample [string]\tSample name to be added to the SAM header (optional).\n");
  fprintf(stderr," --rg [string]\t\tRead group ID to be added to the SAM header (optional).\n");
  fprintf(stderr," --lib [string]\t\tLibrary name to be added to the SAM header (optional).\n");
  fprintf(stderr,"\n\n");
}