patch --progress build_maps

Author: Nicolas Servant

scripts/bowtie_wrap.sh

@@ -139,10 +139,10 @@ if [[ ${MODE} == 'global' ]]; then
 	echo $R2
 	echo "-------------"
 
-	if [[ ! -e $R1 || ! -e $R2 ]]; then
-	    echo "error - input files not found." >&2
-	    exit 1
-	fi
+	#if [[ ! -e $R1 || ! -e $R2 ]]; then
+	#    echo "error - input files not found." >&2
+	#    exit 1
+	#fi
 
 	sample_dir=$(get_sample_dir $r)
 	prefix1=$(basename ${R1} | sed -e 's/.fastq\(.gz\)*//')

scripts/build_raw_maps.sh

@@ -85,7 +85,8 @@ do
 		    cat ${DATA_DIR}/${RES_FILE_NAME}/${RES_FILE_NAME}_allValidPairs | ${SCRIPTS}/build_matrix --binfile ${GENOME_FRAGMENT_FILE} --chrsizes $GENOME_SIZE_FILE --ifile /dev/stdin --oprefix ${MATRIX_DIR}/${bsize}/${RES_FILE_NAME}_${bsize} --matrix-format ${MATRIX_FORMAT} 2> ${LDIR}/build_raw_maps.log
 		## Bin resolution
 		else
-		    cat ${DATA_DIR}/${RES_FILE_NAME}/${RES_FILE_NAME}_allValidPairs | ${SCRIPTS}/build_matrix --binsize ${bsize} --chrsizes $GENOME_SIZE_FILE --ifile /dev/stdin --oprefix ${MATRIX_DIR}/${bsize}/${RES_FILE_NAME}_${bsize} --matrix-format ${MATRIX_FORMAT}  --progress 2> ${LDIR}/build_raw_maps.log
+		    echo " cat ${DATA_DIR}/${RES_FILE_NAME}/${RES_FILE_NAME}_allValidPairs | ${SCRIPTS}/build_matrix --binsize ${bsize} --chrsizes $GENOME_SIZE_FILE --ifile /dev/stdin --oprefix ${MATRIX_DIR}/${bsize}/${RES_FILE_NAME}_${bsize} --matrix-format ${MATRIX_FORMAT} 2> ${LDIR}/build_raw_maps.log"
+		    cat ${DATA_DIR}/${RES_FILE_NAME}/${RES_FILE_NAME}_allValidPairs | ${SCRIPTS}/build_matrix --binsize ${bsize} --chrsizes $GENOME_SIZE_FILE --ifile /dev/stdin --oprefix ${MATRIX_DIR}/${bsize}/${RES_FILE_NAME}_${bsize} --matrix-format ${MATRIX_FORMAT} 2> ${LDIR}/build_raw_maps.log
 		fi
 	    fi
 	done