Creates a profile file for SimSeq, given a BAM alignment and a set of references in FASTA format. Only conserved regions across the references are taken into consideration.
- JDK 7 (http://jdk7.java.net/)
java -jar ProfileSim.jar -i alignment.bam -g references.fasta
java -jar ProfileSim.jar -i alignment.bam -g references.fasta -r 300-4590
#####To minimize the memory consumption and the number of full garbage collector executions, use:
java -XX:NewRatio=9 -jar ProfileSim.jar
#####If your dataset is very large and you run out of memory, increase the heapspace with:
java -XX:NewRatio=9 -Xms2G -Xmx10G -jar ProfileSim.jar
####On multicore systems:
java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar ProfileSim.jar
####On multi-CPU systems:
java -XX:+UseParallelGC -XX:+UseNUMA -XX:NewRatio=9 -Xms2G -Xmx10G -jar ProfileSim.jar
#####Unix wrapper:
function psim() { java -XX:+UseParallelGC -Xms2g -Xmx10g -XX:+UseNUMA -XX:NewRatio=9 -jar ~/ProfileSim.jar $*; }
Help can be shown by running without additional parameters:
java -jar ProfileSim.jar
- Maven 3 (http://maven.apache.org/)
cd ProfileSim
mvn -DartifactId=samtools -DgroupId=net.sf -Dversion=1.8.9 -Dpackaging=jar -Dfile=src/main/resources/jars/sam-1.89.jar -DgeneratePom=false install:install-file
mvn clean package
java -jar ProfileSim/target/ProfileSim.jar
Armin Töpfer
armin.toepfer (at) gmail.com
http://www.bsse.ethz.ch/cbg/people/toepfera
GNU GPLv3 http://www.gnu.org/licenses/gpl-3.0