Running FRC now works

FRC_heinz.sh

@@ -17,7 +17,10 @@ done
 DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
 # Use a single file for logging, use the starttime as identifier
 LOGFILE="FRC_heinz."`date +%Y%m%d_%k%M%S`.out
-
+# EMBOSS path
+export PATH=/home/assembly/bin/haars001/bin:$PATH
+#FRC path
+export PATH=/home/jvh/code/FRC_align/src:$PATH
 # Input assembly
 #allpaths       /home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
 #allpaths_454   /home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw_with454/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
@@ -27,13 +30,15 @@ LOGFILE="FRC_heinz."`date +%Y%m%d_%k%M%S`.out
 
 ASSEMBLY=/home/assembly/dev_150/assemblies/allpaths_lg_sample_heinz_raw/sl/data/run/ASSEMBLIES/test/final.assembly.fasta
 PREFIX=allpaths_lg
+ASSEMBLY=/home/assembly/dev_150/assemblies/clc-default/clc_contigs.fa
+PREFIX=clc
 MIN_PE_INS=320
 MAX_PE_INS=430
 MIN_MP_INS=2435
 MAX_MP_INS=3555
 ESTIMATED_GENOME_SIZE=760000000
 OUTPUT_HEADER=${PREFIX}.FRC.
-
+	
 # Map reads against assembly with BWA
 # Create index
 if [ ! -f ${PREFIX}.bwt ]
@@ -103,15 +108,15 @@ fi
 	samtools index ${PREFIX}.PE.sorted.bam
 
 # run FRC as per README
-FRC 	--pe-sam ${PREFIX}.PE.sorted.ba \
+FRC 	--pe-sam ${PREFIX}.PE.sorted.bam \
 	--pe-min-insert $MIN_PE_INS \
 	--pe-max-insert $MAX_PE_INS \
 	--mp-sam ${PREFIX}.MP.bam \
 	--mp-min-insert $MIN_MP_INS \
 	--mp-max-insert $MAX_MP_INS \
 	--genome-size $ESTIMATED_GENOME_SIZE \
-	--output $OUTPUT_HEADER \
-
+	--output $OUTPUT_HEADER
+exit;
 # TODO : Create better CE statisitcs