doBWAQualTrimming.c

/*
    qaTools - Just more qa tools.
    Copyright (C) 2011  P. Costea(paul.igor.costea@scilifelab.se)

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU Affero 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 Affero General Public License for more details.                  

    You should have received a copy of the GNU Affero General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include "pol_fastq.h"

static void usage()
{
  fprintf(stderr, "\nVersion: 1.4\n");
  fprintf(stderr, "Contact: Paul Costea <paul.igor.costea@scilifelab.se>\n\n");
  fprintf(stderr, "Usage: ");
  fprintf(stderr, "doBWAQualTrimming [Options] <in.fastq> <out.fastq>\n");
  fprintf(stderr, "Options:\n");
  fprintf(stderr, "         -p            Input is a paierd library\n");
  fprintf(stderr, "                       Use: doBWAQualTrimming [Options] <in1.fastq> <in2.fastq> <out1.fastq> <out2.fastq>\n");
  fprintf(stderr, "         -i            Print interwoven output to stdout\n");
  fprintf(stderr, "                       Only for paired end. Use: [...] <in1.fastq> <in2.fastq>\n");
  fprintf(stderr, "         -s            Use solexa qualitites\n");
  fprintf(stderr, "         -v            Write discarded sequences\n");
  fprintf(stderr, "         -a            Write fasta output\n");
  fprintf(stderr, "         -f            Replace discarded sequences with N's\n");
  fprintf(stderr, "         -n            Only remove N's from sequence. -q will be ignored.\n");
  fprintf(stderr, "         -q [INT]      Quality threshold [20]\n");
  fprintf(stderr, "         -l [INT]      Lenght cutoff [50]\n\n");
}

int main(int argc, char* argv[])
{
  char arg;
  int qual = 20;
  int min_length = 50;
  bool onlyN = false;
  bool isPairedLib = false;
  bool writeDropped = false;
  bool isSolexa = false;
  bool replaceWithFake = false;
  bool writeFasta = false;
  bool inter = false;
  //Get args
  while ((arg = getopt(argc, argv, "q:l:psiafvn")) >= 0) {
    switch (arg) {
    case 'q': qual = atoi(optarg); break;
    case 'l': min_length = atoi(optarg); break;
    case 'p': isPairedLib = true; break;
    case 'n': onlyN = true; break;
    case 'v': writeDropped = true; break;
    case 's': isSolexa = true; break;
    case 'a': writeFasta = true; break;
    case 'f': replaceWithFake = true; break;
    case 'i': inter = true; break;
    default: fprintf(stderr,"Wrong parameter input: %s\n",optarg); break;
    }
  }

  if (isPairedLib && inter) {
	if (argc-optind != 2) {
		usage();
		return 1;
	}
  } else if (argc-optind != ((isPairedLib) ? 4 : 2)) {
    usage();
    return 1;
  }

  int p = optind;

  FILE* fast_q1 = fopen(argv[p],"r");
  if (fast_q1 == NULL) {
    printf("Cannot open file %s\n", argv[p]);
    return 1;
  }
  p++;
  FILE* fast_q2 = NULL;
  if (isPairedLib) {
    fast_q2 = fopen(argv[p],"r");
    if (fast_q2 == NULL) {
      printf("Cannot open file %s\n", argv[p]);
      return 1;
    }
    p++;
  }
  FILE* fast_q_out1 = stdout;
  if (!inter) {
     fast_q_out1 = fopen(argv[p],"w");
  }
  if (fast_q_out1 == NULL) {
    printf("Cannot create output file %s\n", argv[p]);
    return 1;
  }
  p++;

  FILE* drop1 = NULL;
  FILE* drop2 = NULL;

  FILE* fast_q_out2 = NULL;
  if (isPairedLib && !inter) {
    fast_q_out2 = fopen(argv[p],"w");
    if (fast_q_out2 == NULL) {
      printf("Cannot create output file %s\n", argv[p]);
    }
  }

  if (writeDropped) {//Open files for writing dropped reads
    if (isPairedLib) {
      drop1 = fopen("dropped1.out","w");
      drop2 = fopen("dropped2.out","w");
    } else {
      drop1 = fopen("dropped.out","w");
    }
  }

  long dropped = 0;
  long count = 0;

  pol_util::FastqEntry* entry1 = NULL;
  pol_util::FastqEntry* entry2 = NULL;

  bool keepGoing = true;
  while (keepGoing) {
    ++count;
    entry1 = pol_util::FastqEntry::readEntry(fast_q1);
    keepGoing = (entry1 != NULL);
    if (isPairedLib) 
      entry2 = pol_util::FastqEntry::readEntry(fast_q2);

    if (!keepGoing)
      break;

    if (onlyN == true) {
      bool rem1,rem2;
      rem1 = entry1->removePoly('N',min_length);
      if (isPairedLib){
	rem2 = entry2->removePoly('N',min_length);
      }
      if ((!rem1) || (isPairedLib && !rem2)) {
	++dropped;
	if (writeDropped) {
	  entry1->write(drop1);
	  if (isPairedLib) {
	    entry2->write(drop2);
	  }
	}
	delete entry1;
	delete entry2;
	continue;
      }
    }else {
      bool trim1,trim2;
      trim1 = entry1->trim(qual,min_length,isSolexa);
      if (isPairedLib)
	trim2 = entry2->trim(qual,min_length,isSolexa);
      if (!trim1 || ( isPairedLib && !trim2 )) {
	++dropped;
	if (writeDropped) {
	  entry1->write(drop1);
	  if (isPairedLib) {
	    //Write second entry
	    entry2->write(drop2);
	  }
	}
	if (replaceWithFake) {//Still print these to the output fastq
	  if (!trim1)
	    entry1->writeFake(fast_q_out1);
	  if (isPairedLib && !trim2)
	    entry2->writeFake(fast_q_out2);
	}
	delete entry1;
	delete entry2;
	continue;
      }
    }

    //Write them to the output files.
    if (writeFasta) {
      entry1->writeFasta(fast_q_out1);
    } else {
      entry1->write(fast_q_out1);
    }
    if (isPairedLib) {
      //Write second entry
      if (writeFasta) {
	entry2->writeFasta(fast_q_out2); 
      } else {
	if (!inter) {
		entry2->write(fast_q_out2);
	} else {
		entry2->write(fast_q_out1);//Write to same output!
	}
      }
    }
    delete entry1;
    delete entry2;
  }

  fclose(fast_q1);
  fclose(fast_q_out1);
  if (isPairedLib) {
    fclose(fast_q2);
    if (!inter) {
    	fclose(fast_q_out2);
    }
  }
  if (writeDropped) {
    fclose(drop1);
    if (isPairedLib)
      fclose(drop2);
  }

  fprintf(stderr,"\n");
  fprintf(stderr,"%ld reads have been dropped!\n",dropped);
  fprintf(stderr,"You just lost about %3.2f procent of your data!\n",(double(dropped)/count)*100);

}