Further changes to convert bam files not generated by fastq2bam

nunofonseca · Feb 11, 2019 · 56b0504 · 56b0504
1 parent 2fc2f21
commit 56b0504
Showing 1 changed file with 22 additions and 20 deletions.
diff --git a/src/bam2fastq.c b/src/bam2fastq.c
@@ -54,9 +54,9 @@ char *get_tag(bam1_t *aln,const char tagname[2]) {
   return(s2);
 }
 
-void QWRITE(gzFile fd,FILE_LOC type, char*s1,char*s2,char*s3) {
+void QWRITE(gzFile fd,FILE_LOC type, char*s1,char*s2,char*s3,int add_suffix) {
   char rn_suf[4]="";
-  if (type!=SE) // add a suffix
+  if (add_suffix) // add a suffix
     sprintf(&rn_suf[0],"/%u",(short)type+1);
   GZ_WRITE(fd,"@");
   GZ_WRITE(fd,s1);
@@ -214,6 +214,7 @@ int main(int argc, char *argv[])
        // ORIG_RN_TAG missing
        // BAM was not generated with fastq2bam
        char *hdr=bam1_qname(aln);
+       qual=get_qual(aln,&qual_buf[0]);
        if ( qual == NULL ) {
 	 // create a dummy sequence to ensure that the fastq file is valid
 	 unsigned int i,len = aln->core.l_qseq;
@@ -234,34 +235,35 @@ int main(int argc, char *argv[])
        } else if ( (aln->core.flag==(BAM_FUNMAP|BAM_FMUNMAP|BAM_FPAIRED|BAM_FREAD1)) || aln->core.flag & BAM_FUNMAP )  {
 	 write_to=R1;
        } 
-       QWRITE(get_fp(fd, write_to , out_file_prefix),write_to, hdr,seq,qual);
+       QWRITE(get_fp(fd, write_to , out_file_prefix),write_to, hdr,seq,qual,TRUE);
      } else {
        // bam generated by fastq2bam 
-       // TODO: add checks?     
-       if ( is_pe == -1 ) {
-	 fprintf(stderr,"processing fastq2bam file...\n");
-	 if (aln->core.flag & BAM_FUNMAP ) {  // SE
-	   is_pe=FALSE;
-	 } else { // PE
-	   if (aln->core.flag & BAM_FPAIRED ) {  
-	     is_pe=TRUE;
-	   }
-	 }
+       // TODO: add checks?
+
+       is_pe=FALSE;
+       if (aln->core.flag & BAM_FPAIRED ) {
+	 is_pe=TRUE;
        }
-       if ( (aln->core.flag==(BAM_FUNMAP|BAM_FMUNMAP|BAM_FPAIRED|BAM_FREAD1)) || aln->core.flag & BAM_FUNMAP )  {
-	 // read1
-	 QWRITE(get_fp(fd, R1 , out_file_prefix),R1, hdr,seq,qual);
+
+       if (  !is_pe  ||
+	    (aln->core.flag & BAM_FREAD1 ) ) {
+	 // 
+	 short write_to=R1;       
+	 if ( ! is_pe )
+	   write_to=SE;
+
+	 QWRITE(get_fp(fd, write_to , out_file_prefix),R1, hdr,seq,qual,FALSE);
 	 // cell
 	 if (get_tag(aln,CELL_TAG)!=NULL)
-	   QWRITE(get_fp(fd, CELL, out_file_prefix),CELL, hdr,get_tag(aln,CELL_TAG),get_tag(aln,CELL_QUAL_TAG));
+	   QWRITE(get_fp(fd, CELL, out_file_prefix),CELL, hdr,get_tag(aln,CELL_TAG),get_tag(aln,CELL_QUAL_TAG),FALSE);
 	 // umi
 	 if (get_tag(aln,UMI_TAG)!=NULL)
-	   QWRITE(get_fp(fd, UMI, out_file_prefix),UMI,hdr,get_tag(aln,UMI_TAG),get_tag(aln,UMI_QUAL_TAG));
+	   QWRITE(get_fp(fd, UMI, out_file_prefix),UMI,hdr,get_tag(aln,UMI_TAG),get_tag(aln,UMI_QUAL_TAG),FALSE);
 	 // sample
 	 if (get_tag(aln,SAMPLE_TAG)!=NULL)
-	   QWRITE(get_fp(fd, SAMPLE, out_file_prefix),SAMPLE,hdr,get_tag(aln,SAMPLE_TAG),get_tag(aln,SAMPLE_QUAL_TAG));
+	   QWRITE(get_fp(fd, SAMPLE, out_file_prefix),SAMPLE,hdr,get_tag(aln,SAMPLE_TAG),get_tag(aln,SAMPLE_QUAL_TAG),FALSE);
        } else { //R2
-	 QWRITE(get_fp(fd, R2 , out_file_prefix),R2,hdr,seq,qual);
+	 QWRITE(get_fp(fd, R2 , out_file_prefix),R2,hdr,seq,qual,FALSE);
        }
      }
   }