--- a/freebayes.xml	Wed Feb 08 12:45:05 2017 -0500
+++ b/freebayes.xml	Thu May 04 11:34:13 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2">
+<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-3">
     <description>bayesian genetic variant detector</description>
     <macros>
         <import>macros.xml</import>
@@ -35,14 +35,25 @@
         ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
     #end if
 
-    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
-        samtools view -H b_${bam_count}.bam |
-        grep "^@SQ" |
-        cut -f 2- |
-        awk '{ gsub("^SN:","",$1);
-        gsub("^LN:","",$2);
-        print $1"\t0\t"$2; }' >> regions_all.bed &&
-    #end for
+    ##if user has specified a region or target file, just use instead of calculating a set of unique regions
+
+    #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
+        ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
+    #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
+        printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
+    #else
+        ##divide up the regions in the bam file for efficient processing
+        #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
+            samtools view -H b_${bam_count}.bam |
+            grep "^@SQ" |
+            cut -f 2- |
+            awk '{ gsub("^SN:","",$1);
+            gsub("^LN:","",$2);
+            print $1"\t0\t"$2; }' >> regions_all.bed &&
+        #end for
+    #end if
+
+
 
     sort -u regions_all.bed > regions_uniq.bed &&
     ## split into even small chunks, this has some disatvantages and will not be used for the moment
@@ -73,12 +84,6 @@
         ## Outputs
         --vcf './vcf_output/part_\$i.vcf'
 
-        #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
-            --targets '${target_limit_type.input_target_bed}'
-        #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
-            --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
-        #end if
-
         ##advanced options
         #if str( $options_type.options_type_selector ) == "simple":
             ##do nothing as command like build up to this point is sufficinet for simple diploid calling