+ interesting version : it crashes but valgrind detects 0 errors

git-svn-id: http://svn.tuebingen.mpg.de/ag-raetsch/projects/QPalma@9878 e1793c9e-67f9-0310-80fc-b846ff1f7b36

diff --git a/tools/data_tools/filterReads.c b/tools/data_tools/filterReads.c
index 84e45ae..2dba63a 100644 (file)
--- a/tools/data_tools/filterReads.c
+++ b/tools/data_tools/filterReads.c
@@ -481,7 +481,6 @@ int join_reads(int exon_stop, int exon_start, Read* up_read, Read* down_read, FI
    int down_range = down_read_stop - exon_start + 1;
    int retval;
 
-
    int u_size, d_size;
    u_size = d_size = -1;
 
@@ -505,9 +504,7 @@ int join_reads(int exon_stop, int exon_start, Read* up_read, Read* down_read, FI
    int u_off = p_start - up_read_start;
    int d_off = exon_start - down_read_start;
 
-   FA(u_off >= 0);
-   FA(d_off >= 0);
-
+   FA(u_off >= 0 && d_off >= 0);
    FA( exon_stop - p_start + p_stop - exon_start + 2 == read_size);
    FA( u_size + d_size == read_size );
 
@@ -517,16 +514,42 @@ int join_reads(int exon_stop, int exon_start, Read* up_read, Read* down_read, FI
    char* new_seq = malloc(sizeof(char)*buf_size);
    memset(new_seq,'z',sizeof(char)*buf_size);
 
+   if ( current_strand == 'P' ) {
+      printf("flipping read sequences...\n");
+      printf("%s %s\n",up_read->seq,down_read->seq);
+
+      char *tmp = malloc(sizeof(char)*strlen(up_read->seq+1));
+      strncpy(tmp,up_read->seq,strlen(up_read->seq));
+      tmp[strlen(up_read->seq)]='\0';
+      realloc(up_read->seq,sizeof(char)*strlen(down_read->seq+1));
+      strncpy(up_read->seq,down_read->seq,strlen(down_read->seq));
+      up_read->seq[strlen(down_read->seq)] = '\0';
+      realloc(down_read->seq,sizeof(char)*strlen(tmp));
+      strncpy(down_read->seq,tmp,strlen(tmp));
+      down_read->seq[strlen(tmp)] = '\0';
+
+      free(tmp);
+
+      printf("flipping done...\n");
+      printf("%s %s\n",up_read->seq,down_read->seq);
+   }
+
+   printf("start joining...\n");
    Tuple jinfo = join_seq(new_seq,up_read->seq,u_off,u_size,down_read->seq,d_off,d_size,down_range);
+   printf("end of joining...\n");
 
    int cut_pos = jinfo.first;
    int additional_pos = jinfo.second;
+   printf("jinfo contains %d/%d\n",jinfo.first,jinfo.second);
 
    buf_size = read_size+1+additional_pos;
 
+   printf("allocating quality arrays (size=%d)...\n",buf_size);
    char* new_prb        = malloc(sizeof(char)*buf_size);
    char* new_cal_prb    = malloc(sizeof(char)*buf_size);
    char* new_chastity   = malloc(sizeof(char)*buf_size);
+   if (new_prb == NULL || new_cal_prb == NULL || new_chastity == NULL)
+      perror("malloc\n");
 
    if( jinfo.first == -1 ) {
       retval = 0;
@@ -538,30 +561,34 @@ int join_reads(int exon_stop, int exon_start, Read* up_read, Read* down_read, FI
       goto free;
    }
 
+   printf("joining qualities...\n");
    strncpy(new_prb, up_read->prb+u_off, u_size);
    strncpy(new_prb+u_size, down_read->prb+d_off, d_size+additional_pos);
-   new_prb[read_size+additional_pos] = '\0';
+   new_prb[buf_size] = '\0';
 
    strncpy(new_cal_prb, up_read->cal_prb+u_off, u_size);
    strncpy(new_cal_prb+u_size, down_read->cal_prb+d_off, d_size+additional_pos);
-   new_cal_prb[read_size+additional_pos] = '\0';
+   new_cal_prb[buf_size] = '\0';
 
    strncpy(new_chastity, up_read->chastity+u_off, u_size);
    strncpy(new_chastity+u_size, down_read->chastity+d_off, d_size+additional_pos);
-   new_chastity[read_size+additional_pos] = '\0';
+   new_chastity[buf_size] = '\0';
+   printf("end of joining qualities...\n");
 
    //printf("old reads: %s %s (%d %d %d/%d)\n",up_read->seq,down_read->seq,up_read->pos,down_read->pos,u_off,d_off);
    //printf("new read: %s %d %d\n",new_seq,cut_pos,u_size);
 
-   int alpha   = read_size - u_off - 1;
-   int beta    = alpha - u_size ;
-   p_start     = up_read->pos + beta + 1;
-   exon_stop   = up_read->pos + alpha;
-
-   alpha   = read_size - d_off - 1;
-   beta    = alpha - (read_size - u_size);
-   exon_start  = down_read->pos + beta + 1; 
-   p_stop      = down_read->pos + alpha;
+   //if ( current_strand == 'P' ) {
+   //   int alpha   = read_size - u_off - 1;
+   //   int beta    = alpha - u_size ;
+   //   p_start     = up_read->pos + beta + 1;
+   //   exon_stop   = up_read->pos + alpha;
+
+   //   alpha   = read_size - d_off - 1;
+   //   beta    = alpha - (read_size - u_size);
+   //   exon_start  = down_read->pos + beta + 1; 
+   //   p_stop      = down_read->pos + alpha;
+   //}
 
    int status = 1; //fitting(up_read->prb,down_read->prb,u_off,d_off,u_size,d_size);