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important: checkHitOverlapping; naive doing selectAllTranscripts; all selection modes takes event codes, splice chains and variant lists;

force naive to do clusters

reference argument

Merge branch 'metrics-astafunk' of ssh://sammeth.net:7999/barna/barna into metrics-astafunk

reverse comparator

new termination for astafunk threads;

create checkHitOverlapping

clean

HitComparator in the end; remove sequence length correction; changed scorePath

check

check whether new hit is added

check whether a new hit is added

check whether a new hit is added

silence call()

added the "clean mode" output; naive methods

added the "clean mode" output; AllTranscriptHits is default now

added the "clean mode" output

added the "clean mode" output

unique output print method; moved createDomainCluster here

createDomainCluster moved to Utils

added the "clean mode" output

create unique output method;

number of analysed genes, events, transcripts and domains

call to run

change visibility of isConstitutive

removed stupid things

better

set merged variant

test

setTranscriptID