sonicationSize flag name change to ampliconSize

Hughes-Genome-Group · Apr 18, 2018 · e46a5d6 · e46a5d6
1 parent 57ecf3b
commit e46a5d6
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/bin/bashHelpers/runscript.sh b/bin/bashHelpers/runscript.sh
@@ -71,8 +71,8 @@ intQuals=33
 
     echo "Flash will be ran in quality score scheme : ${intQuals}"
 
-echo "flash -x ${flashX} -M $((${SONICATIONSIZE}+50)) -m ${FLASHOVERLAP} -p ${intQuals} READ1.fastq READ2.fastq"
-flash -x ${flashX} -M $((${SONICATIONSIZE}+50)) -m ${FLASHOVERLAP} -p ${intQuals} READ1.fastq READ2.fastq > flashing.log
+echo "flash -x ${flashX} -M $((${AMPLICONSIZE}+50)) -m ${FLASHOVERLAP} -p ${intQuals} READ1.fastq READ2.fastq"
+flash -x ${flashX} -M $((${AMPLICONSIZE}+50)) -m ${FLASHOVERLAP} -p ${intQuals} READ1.fastq READ2.fastq > flashing.log
 
 cat flashing.log
 

diff --git a/bin/bashHelpers/usageAndVersion.sh b/bin/bashHelpers/usageAndVersion.sh
@@ -52,7 +52,7 @@ echo "--lanes 1 (set this to be the number of lanes, if there are more than 1 la
 echo ""
 echo "LIBRARY : FRAGMENT LENGHT SETTINGS"
 # --flashX (hidden flag) 0 (how many mismatches allowed in flash step - by default zero, and actually no reason to change this.)
-echo "--sonicationSize 300 (Max expected size of a flash-combined fragment). Check the correctness of the parameter you gave here, after the run, from the fastQC report of the flashed reads."
+echo "--ampliconSize 300 (Max expected size of a flash-combined fragment). Check the correctness of the parameter you gave here, after the run, from the fastQC report of the flashed reads."
 echo
 echo "--flashOverlap 40    (Only affects the visualisation - How much the reads need to overlap, before they are combined to R1-R2 flashed read. Default super stringent 40 bases. "
 echo "                      The rest of the reads continue as non-flashed reads - i.e. this only affects the visualisation part of the analysis. )"

diff --git a/plateScreen96.sh b/plateScreen96.sh
@@ -116,7 +116,7 @@ SINGLE_END=0
 GENOME="UNDEFINED"
 
 flashX=0
-SONICATIONSIZE=300
+AMPLICONSIZE=300
 FLASHOVERLAP=40
 MINPCRCOUNT=100
 MAXPERWELL=20
@@ -271,7 +271,7 @@ minMatch=1
 #------------------------------------------
 
 
-OPTS=`getopt -o h,g: --long help,lanes:,singleEnd,gz,flashX:,sonicationSize:,flashOverlap:,minPCRcount:,minLen:,minLen8:,minLen12:,maxPerWell:,stepSize:,tileSize:,minScore:,minIdentity:,minMatch: -- "$@"`
+OPTS=`getopt -o h,g: --long help,lanes:,singleEnd,gz,flashX:,ampliconSize:,flashOverlap:,minPCRcount:,minLen:,minLen8:,minLen12:,maxPerWell:,stepSize:,tileSize:,minScore:,minIdentity:,minMatch: -- "$@"`
 if [ $? != 0 ]
 then
     usage ;
@@ -288,7 +288,7 @@ while true ; do
         --singleEnd) SINGLE_END=1 ; shift;;
         --gz) GZIP=1 ; shift;;
         --flashX) flashX=$2 ; shift 2;;
-        --sonicationSize) SONICATIONSIZE=$2 ; shift 2;;
+        --ampliconSize) AMPLICONSIZE=$2 ; shift 2;;
         --flashOverlap) FLASHOVERLAP=$2 ; shift 2;;
         --minPCRcount) MINPCRCOUNT=$2 ; shift 2;;
         --minLen) minLen=$2 ; shift 2;;
@@ -419,7 +419,7 @@ echo "GZIP ${GZIP}"
 # echo "SINGLE_END ${SINGLE_END}"
 echo
 echo "flashX ${flashX} "
-echo "SONICATIONSIZE ${SONICATIONSIZE}"
+echo "AMPLICONSIZE ${AMPLICONSIZE}"
 echo "FLASHOVERLAP ${FLASHOVERLAP}"
 echo "MINPCRCOUNT ${MINPCRCOUNT}"
 echo "MINLENfwd ${MINLEN8}"
@@ -443,7 +443,7 @@ echo "GZIP ${GZIP}" >> ${SUMMARYFILE}
 # echo "SINGLE_END ${SINGLE_END}" >> ${SUMMARYFILE}
 echo >> ${SUMMARYFILE}
 echo "flashX ${flashX} " >> ${SUMMARYFILE}
-echo "SONICATIONSIZE ${SONICATIONSIZE}" >> ${SUMMARYFILE}
+echo "AMPLICONSIZE ${AMPLICONSIZE}" >> ${SUMMARYFILE}
 echo "FLASHOVERLAP ${FLASHOVERLAP}" >> ${SUMMARYFILE}
 echo "MINPCRCOUNT ${MINPCRCOUNT}" >> ${SUMMARYFILE}
 echo "MINLENfwd ${MINLEN8}" >> ${SUMMARYFILE}