<commit_before># Demonstration command line for ABRA.
# bwa mem and a recent version of java must be in your command path
# Assumes your current working directory is the demo directory

# Path to ABRA jar file (with dependencies)
# If you've downloaded the jar, set this to the appropriate location
# Compiled jars will be under the target directory
JAR=../target/abra-0.79-SNAPSHOT-jar-with-dependencies.jar

# Path to hg19 reference (indexed by BWA)
#REF=/datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/ref/GRCh37-lite.fa
REF=<path to hg19 reference>

echo "ABRA demo starting..."

java -Xmx4G -jar $JAR --ref $REF --in abra_demo.bam --out abra_demo_realigned.bam --kmer 43,53,63,73,83 --working abra_temp_dir --targets demo.bed > abra_demo.log 2>&1

echo "ABRA demo done.  Realigned BAM: abra_demo_realigned.bam.  Sort and index the realigned BAM if you'd like to view it."<commit_msg>Removed kmers param from demo.<commit_after># Demonstration command line for ABRA.
# bwa mem and a recent version of java must be in your command path
# Assumes your current working directory is the demo directory

# Path to ABRA jar file (with dependencies)
# If you've downloaded the jar, set this to the appropriate location
# Compiled jars will be under the target directory
JAR=../target/abra-0.79-SNAPSHOT-jar-with-dependencies.jar

# Path to hg19 reference (indexed by BWA)
#REF=/datastore/rclbg/nextgenout3/MOSE_TEST/abra/brca/ref/GRCh37-lite.fa
REF=<path to hg19 reference>

echo "ABRA demo starting..."

java -Xmx4G -jar $JAR --ref $REF --in abra_demo.bam --out abra_demo_realigned.bam --working abra_temp_dir --targets demo.bed > abra_demo.log 2>&1

echo "ABRA demo done.  Realigned BAM: abra_demo_realigned.bam.  Sort and index the realigned BAM if you'd like to view it."
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{'dir': 'git-commits-cleaned', 'id': '2587337', 'n_tokens_mistral': 631, 'n_tokens_neox': 598, 'n_words': 219}