MiXCR execution script now passes java-specific options directly to JVM.

This fixes #29

CHANGELOG_CURRENT

@@ -1,5 +1,6 @@
 New feature: optional short column names in `export...` action to simplify further data analysis using data table processing libraries like Pandas or R/DataFrames. (`-s` / `--no-spaces` in `exportAlignments` and `exportClones`)
 New export fields: `-defaultAnchorPoints` outputs positions of default anchor point in aligned reads or clonal sequence (this column is added to default output format), `-positionOf` outputs position of specified anchor point, `-lengthOf` outputs lengt of specified gene feature
+MiXCR execution script now passes java-specific options directly to JVM (e.g. you can execute `mixcr -Xmx2g align ...`)
 Added `V5UTRBeginTrimmed` anchor point, `V5UTR` gene feature renamed to `V5UTRGermline`, trimmed `V5UTR` gene feature added
 Added `--filter-out-of-frames` and `--filter-stops` options in `exportClones`
 minor: some column names in output tab-delimited files slightly changed

mixcr

@@ -36,23 +36,56 @@ case $os in
     ;;
 esac
 
-targetXmx=12000
+mixcrArgs=()
+javaArgs=()
 
-if [[ $targetXmx -gt $maxMb ]];
-then
-    targetXmx=$maxMb
-fi
+needXmxXms=true
+
+while [[ $# > 0 ]]
+do
+    key="$1"
+    shift
+    case $key in
+        -D*|-X*)
+            javaArgs+=(${key})
 
-targetXms=$((${targetXmx}*2/3))
+            case $key in
+                -Xmx*|-Xms*)
+                    needXmxXms=false
+                    ;;
+            esac
 
-if [[ $targetXms -lt 2000 ]];
+            ;;
+        *)
+            mixcrArgs+=(${key})
+            ;;
+    esac
+done
+
+if [[ ${needXmxXms} == true ]]
 then
-    targetXms=$targetXmx
+    targetXmx=12000
+
+    if [[ $targetXmx -gt $maxMb ]];
+    then
+        targetXmx=$maxMb
+    fi
+
+    javaArgs+=("-Xmx${targetXmx}m")
+
+    targetXms=$((${targetXmx}*2/3))
+
+    if [[ $targetXms -lt 2000 ]];
+    then
+        targetXms=$targetXmx
+    fi
+
+    javaArgs+=("-Xms${targetXms}m")
 fi
 
 jar=""
 
-for j in "$DIR/../jar/mixcr.jar" "$DIR/mixcr.jar" "$DIR/target/mixcr-1.2-distribution.jar"
+for j in "$DIR/../jar/mixcr.jar" "$DIR/mixcr.jar" $(ls -d -1 $DIR/target/* 2> /dev/null | grep distribution.jar)
 do
     if [[ -e "$j" ]];
     then
@@ -67,4 +100,4 @@ then
     exit 1
 fi
 
-$java -Dmixcr.command=mixcr -Xmx${targetXmx}m -Xms${targetXms}m -XX:+AggressiveOpts -jar $jar "${@:1}"
+$java -Dmixcr.command=mixcr -XX:+AggressiveOpts "${javaArgs[@]}" -jar $jar "${mixcrArgs[@]}"