elandParser.c

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#include "format.h"
#include "log.h"
#include "linestream.h"
#include "common.h"
#include "elandParser.h"



static LineStream ls = NULL;



void elandParser_init (char *fileName)
{
  ls = ls_createFromFile (fileName);
}



void elandParser_deInit (void)
{
  ls_destroy (ls);
}



static void elandParser_freeQuery (ElandQuery *currElandQuery) 
{
  if (currElandQuery == NULL) {
    return;
  }
  hlr_free (currElandQuery->sequenceName);
  hlr_free (currElandQuery->sequence);
  hlr_free (currElandQuery->matchCode);
  if (currElandQuery->chromosome != NULL) {
    hlr_free (currElandQuery->chromosome);
  }
  freeMem (currElandQuery);
}



ElandQuery* elandParser_nextQuery (void)
{
  WordIter w;
  char *line,*token,*pos;
  static ElandQuery *currElandQuery = NULL;
   
  while (line = ls_nextLine (ls)) {
    if (line[0] == '\0') {
      continue;
    }
    elandParser_freeQuery (currElandQuery);
    currElandQuery = NULL;
    AllocVar (currElandQuery);
    w = wordIterCreate (line,"\t",0);
    currElandQuery->sequenceName = hlr_strdup (wordNext (w) + 1); // remove the '>' character at beginning of the line
    currElandQuery->sequence = hlr_strdup (wordNext (w));
    currElandQuery->matchCode = hlr_strdup (wordNext (w));
    if (strEqual (currElandQuery->matchCode,"QC")) {
      wordIterDestroy (w);
      return currElandQuery;
    }
    currElandQuery->exactMatches = atoi (wordNext (w));
    currElandQuery->oneErrorMatches = atoi (wordNext (w));
    currElandQuery->twoErrorMatches = atoi (wordNext (w));
    token = wordNext (w);
    if (token == NULL) {
      wordIterDestroy (w);
      return currElandQuery;
    }
    if (!(pos = strchr (token,'.'))) {
      die ("Expected '.' in chromosome name: %s",token);
    }
    *pos = '\0';
    currElandQuery->chromosome = hlr_strdup (pos + 1);
    currElandQuery->position = atoi (wordNext (w));
    token = wordNext (w);
    if (token[0] == 'F') {
      currElandQuery->strand = '+'; 
    }
    else if (token[0] == 'R') {
      currElandQuery->strand = '-'; 
    } 
    wordIterDestroy (w);
    return currElandQuery;
  }
  elandParser_freeQuery (currElandQuery);
  currElandQuery = NULL;
  return currElandQuery;
}

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