# EDITING ONLY BY ADVANCED USERS
# This section contains global constants used by CASAVA

[APP_CONFIGURATION]
TAG_NMNM            notMapped
TAG_noMatch         noMatch
TAG_qcFail          qcFail
TAG_nonUnique       nonUnique
TAG_rm              repeatMasked
TAG_mixed           mixed
TAG_control         control
NMNMSplitSize       25000000
NMNMTasks           8
cmdDelete           rm
cmdExport           sortExport.pl
cmdRunExport        runSortExport.pl
cmdRunSplit         runSplitUnSorted.pl
cmdSort             sort
#cmdSort             /opt/coreutils-7.6/bin/sort
cmdSplit            splitUnSorted.pl
cmdReports          generateReports.pl
cmdStats            generateStats.pl
cmdGff              snp2gff.pl
cmdTaskManager      taskServer.pl
defaultStagesDNApaired  sort,assembleIndels,callSmallVariants
defaultStagesDNAsingle  sort,callSmallVariants
defaultStagesRNAsingle  sort,callSmallVariants,rnaCounts
dirConf             /conf/
dirDup              /export/
dirLibExec          /home/psgendb/local/pkg/CASAVA_v1.8.2-build/libexec/CASAVA-1.8.2
dirToMove           /to_move/
dirBam              bam
f_allele_sort       sort.count
f_reads_indx        Reads.idx
f_unsort            unsort.txt
f_unsort_anom       unsort_anom.txt
f_unsort_orph       unsort_orph.txt
f_gaps_prefix       Gaps_
f_gaps_suffix       .lst
snp_f_suffix        .snp.txt
ucscgaps_f_suffix   _gap.txt
sv_f_dels_prefix    deletions_
sv_f_ins_prefix     insertions_
sv_f_invs_prefix    inversionsFFRR_
sv_f_dups_prefix    duplications_
sv_f_chimeras       chimeras.txt
formatDate          %d-%m-%y
formatTimeStamp     %H_%M_%S_%d_%m_%y
projectConf         project.conf
runConfFileName     run.conf.xml
indelsFileName      indels.txt
stateFinished       finished
spliceJunctionAuto  splice_sites-auto.fa
version             /home/psgendb/local/pkg/CASAVA_v1.8.2-build/libexec/CASAVA-1.8.2
contigNameForbiddenCharacters ?()\[\]/\\=+<>:;\"\',*^&

[PROJECT_CONFIGURATION]
appVersion          CASAVA-1.8.2
binSizeBuild        50000000
binSizeProject      50000000
applicationType     DNA
dirRefSeq
readMode            
read                
barcodes            
lanes               
snpThreshold        10 
snpThreshold2       6
snpMaxRatio         3
QVCutoff            90
QVCutoffSingle      10
verbose             0
isWorkflow          1
isWorkflowAuto      0
isWorkflowSGE       0
sgeQmakeFlags       -cwd -v PATH
makeFlags           
isWorkflowMake      0
task2MakeParams     
readSampleRateStart 1.0
readSampleRateEnd  	1.0
readSampleRateStep  0.1
readSampleRateInput	1.0
qualityType         Phred64
genesListPath       
rmDup               YES
toNMScore           -1
removeTemps         ON
workflowFile        tasks.txt
spliceJunction      splice_sites-auto.fa
featureFileName     
refFlatFile         
indelsSrasThreshold             10
indelsPrasThreshold             6
indelsSpReadThresholdIndels     25.0
indelsSdFlankWeight             5
indelsAlignScoreThresh          100
indelsMinGroupSize              3
indelsSpReadThresholdClusters   5
indelsMinCoverage               1
indelsMinContext                6
alignabilityReadLength          30
alignabilityBatchSize           15000000
alignabilityForceRegenerate     0
alignabilitySuppressWarnings    0
indelsCovCutoff	                3
singleScoreForPE    NO
dataSetSuffix        
jobsLimit
extraBltArgs
dirBuildTemp        $buildDir/tmp
sortBufferSize      1984
sortMaxBatchSize    128

variantsSnpTheta                0.001
variantsIndelTheta              0.0001
variantsSnpCovCutoff            3.0
variantsIndelCovCutoff          3.0
variantsSiteErrorDepDefault     0.6
variantsSiteErrorDepNoMismatch  0.35
variantsMinVexp                 0.25
variantsSummaryMinQsnp          20
variantsSummaryMinQindel        20
variantsMinQbasecall            0
variantsMDFilterCount           2
variantsMDFilterFlank           20
variantsMaxIndelSizeSEDefault   50
variantsMaxIndelSizePEDefault   300

maskRefSeqFiles     *.fa
regExpMitochondria  ^cM.fa$|^chrM.fa$|^cMT.fa$|^chrMT.fa$|^M$|^MT$
rnaCountMethod      readBases

poissonAlnCutoff           24
ignoreMissingMetadata 0

svRank_alnCutoff    24
svRank_covCutoff    10
svRank_DepthWindow  1000
svRank_maxFragmentSize     10000000
svRank_minObservations     5
svRank_minSingleScore      10
svRank_numLongSD           3
svRank_numShortSD          5
svRank_maxSD               100

bamWholeGenome      0
cmdSamtools         /home/psgendb/local/pkg/CASAVA_v1.8.2-build/libexec/CASAVA-1.8.2/samtools

cmdGzip             gzip
cmdGunzip           gunzip

consensusIncludeIndels     0
chromNameSource            fileName
chromNameValidation        on
refSeqCacheDirName         cachedRefSeq

seqGeneMd2RefFlatParams    
nonoverlappingExonCoordsParams --verbose=1