Merge branch 'release/v1.4'

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "milib"]
+	path = milib
+	url = https://github.com/milaboratory/milib.git

CHANGELOG

@@ -1,4 +1,11 @@
 
+MiTools 1.4 (14 Jul 2016)
+========================
+
+-- added new action: `mitools cut` to cut sequences to a fixed or random length (see help `mitools 
+   cut -h`)
+
+
 MiTools 1.3 ( 1 Feb 2016)
 ========================
 

mitools

@@ -0,0 +1,146 @@
+#!/bin/bash
+
+java="java"
+
+sedString="s/.*1\.\(.*\)\..*/\1/"
+jVersion=$($java -version 2>&1 | grep version | awk '{ print $3 }' | sed $sedString)
+if [[ $jVersion -lt 7 ]];
+then
+    echo "Wrong version of java. Please use Java 7 or higher."
+    exit 1
+fi
+
+# Linux readlink -f alternative for Mac OS X
+function readlinkUniversal() {
+    targetFile=$1
+
+    cd `dirname $targetFile`
+    targetFile=`basename $targetFile`
+
+    # iterate down a (possible) chain of symlinks
+    while [ -L "$targetFile" ]
+    do
+        targetFile=`readlink $targetFile`
+        cd `dirname $targetFile`
+        targetFile=`basename $targetFile`
+    done
+
+    # compute the canonicalized name by finding the physical path 
+    # for the directory we're in and appending the target file.
+    phys_dir=`pwd -P`
+    result=$phys_dir/$targetFile
+    echo $result
+}
+
+os=`uname`
+delta=100
+
+dir=""
+
+case $os in
+    Darwin)
+        freeBlocks=$(vm_stat | grep free | awk '{ print $3 }' | sed 's/\.//')
+        inactiveBlocks=$(vm_stat | grep inactive | awk '{ print $3 }' | sed 's/\.//')
+        speculativeBlocks=$(vm_stat | grep speculative | awk '{ print $3 }' | sed 's/\.//')
+        freeMb=$((($freeBlocks+$speculativeBlocks)*4096/1048576))
+        inactiveMb=$(($inactiveBlocks*4096/1048576))
+        maxMb=$((($freeMb+$inactiveMb-$delta)))
+        dir=$(dirname "$(readlinkUniversal "$0")")
+    ;;
+    Linux)
+        rFreeMb=$(free -m | head -n 3 | tail -n 1 | awk '{ print $4 }')
+        maxMb=$(($rFreeMb-$delta))
+        dir="$(dirname "$(readlink -f "$0")")"
+    ;;
+    *)
+       echo "Unknown OS."
+       exit 1
+    ;;
+esac
+
+bin=${dir}/$0
+
+jarBase="mitools"
+
+appArgs=()
+javaArgs=()
+
+needXmxXms=true
+otherJar=""
+
+while [[ $# > 0 ]]
+do
+    key="$1"
+    shift
+    case $key in
+        -D*|-X*|-ea|-agentlib*)
+            javaArgs+=(${key})
+
+            case $key in
+                -Xmx*|-Xms*)
+                    needXmxXms=false
+                    ;;
+            esac
+
+            ;;
+        -jar|-V)
+            otherJar="$1"
+            shift
+            ;;
+        *)
+            appArgs+=("${key}")
+            ;;
+    esac
+done
+
+if [[ ${needXmxXms} == true ]]
+then
+    targetXmx=3000
+
+    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${targetXms}m")
+fi
+
+jar=""
+
+if [[ -z "$otherJar" ]];
+then
+    for j in "$dir/../jar/${jarBase}.jar" "$dir/${jarBase}.jar" $(ls -d -1 $dir/target/* 2> /dev/null | grep distribution.jar)
+    do
+        if [[ -e "$j" ]];
+        then
+            jar=$j
+            break
+        fi
+    done
+else
+    for j in $(ls -1 ${dir}/* | grep "${jarBase}" | grep ".jar" | grep ${otherJar});
+    do
+        if [[ -e "$j" ]];
+        then
+            jar=$j
+            break
+        fi
+    done
+fi
+
+if [[ "$jar" == "" ]];
+then
+    echo "No jar."
+    exit 1
+fi
+
+$java -Dapp.path=$dir -Dapp.command=mixcr -XX:+AggressiveOpts "${javaArgs[@]}" -jar $jar "${appArgs[@]}"

pom.xml

@@ -19,10 +19,10 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mitools</artifactId>
-    <version>1.3</version>
+    <version>1.4</version>
     <packaging>jar</packaging>
     <name>MiTools</name>
-    <url>http://milaboratory.com/</url>
+    <url>https://github.com/milaboratory/mitools</url>
 
     <parent>
         <groupId>org.sonatype.oss</groupId>
@@ -94,7 +94,13 @@
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>milib</artifactId>
-            <version>${project.version}</version>
+            <version>1.5-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>com.beust</groupId>
+            <artifactId>jcommander</artifactId>
+            <version>1.48</version>
+            <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>com.milaboratory</groupId>
@@ -115,16 +121,6 @@
             <version>1.9.5</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>com.beust</groupId>
-            <artifactId>jcommander</artifactId>
-            <version>1.30</version>
-        </dependency>
-        <dependency>
-            <groupId>cc.redberry</groupId>
-            <artifactId>pipe</artifactId>
-            <version>0.9.4</version>
-        </dependency>
     </dependencies>
 
     <properties>
@@ -135,11 +131,6 @@
         <connection>scm:git:https://github.com/milaboratory/mitools.git</connection>
     </scm>
 
-    <issueManagement>
-        <system>YouTrack</system>
-        <url>http://youtrack.milaboratory.com/</url>
-    </issueManagement>
-
     <profiles>
         <profile>
             <id>release</id>