# this will cause the sequence header names to be used as chromosome names
REFERENCE human SAMTOOLS_GENOME /home/psgendb/local/pkg/CASAVA_v1.8.2-build/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/Chromosomes/chr22.fa

# this will cause the sequence file names to be used as chromosome names
REFERENCE phix SAMTOOLS_GENOME /home/psgendb/local/pkg/CASAVA_v1.8.2-build/share/CASAVA-1.8.2/examples/iGenomes/PhiX/NCBI/1993-04-28/Sequence/Chromosomes/phix.fa
REFERENCE phix KAGU_PARAMS --circular phix

REFERENCE human ANALYSIS eland_rna
REFERENCE phix ANALYSIS eland_pair
REFERENCE unknown ANALYSIS none

ELAND_RNA_GENOME_ANNOTATION /home/psgendb/local/pkg/CASAVA_v1.8.2-build/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Annotation/Genes/refFlat.txt.gz
ELAND_RNA_GENOME_CONTAM /home/psgendb/local/pkg/CASAVA_v1.8.2-build/share/CASAVA-1.8.2/examples/iGenomes/Homo_sapiens/UCSC/hg18/Sequence/AbundantSequences

# allow both ends to be processed (off by default)
ELAND_RNA_MULTI_READS on

PAS_PARAMS --max_patterns_to_store 100000