#### references and Parameters

### tools 
SAMTOOLS="@INSTALL_DIR@/bin/samtools" 
BEDTOOLS="@INSTALL_DIR@/bin/bedtools/bin"
BWA="@INSTALL_DIR@/bin/bwa"
PICARD="@INSTALL_DIR@/bin/picard"
PRIMER3="@INSTALL_DIR@/bin/primer3/src/primer3_core"
FANCYBOX="@INSTALL_DIR@/bin/fancybox"
RLIB="@INSTALL_DIR@/Rlibs"
#### executable
PERL="@PERL@"
JAVA="@JAVA@"
R="@R_EXE@"


### references
USER_HUMAN_database="@INSTALL_DIR@/resources/reference.fa"
HUMAN_database="@INSTALL_DIR@/resources/human.fa"
HUMAN_database_Index="@INSTALL_DIR@/resources/human"
VIRUS_database="@INSTALL_DIR@/resources/virus.fa"
VIRUS_database_Index="@INSTALL_DIR@/resources/virus"
VIRUS_HUMAN_database="@INSTALL_DIR@/resources/human_virus.fa"
VIRUS_HUMAN_database_Index="@INSTALL_DIR@/resources/human_virus"
REF_FLAT="@INSTALL_DIR@/resources/refFlat.txt.gz"
HUMAN_CYTOBAND="@INSTALL_DIR@/resources/cytoBand.txt.gz"

### 
THREADS="4"
##lowering this number will give more HGT events 
SEQUENCE_COMPLEXITY="0.7"
DEPTH="5"

### Integration Site parameters
MINRP="1"
MINSOFT="5"
