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Update README
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mourisl committed Sep 6, 2020
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Expand Up @@ -41,6 +41,7 @@ PsiCLASS depends on [pthreads](http://en.wikipedia.org/wiki/POSIX_Threads) and s
-c FLOAT: only use the subexons with classifier score <= than the given number. (default: 0.05)
--sa FLOAT: the minimum average number of supported read for retained introns (default: 0.5)
--vd FLOAT : the minimum average coverage depth of a transcript to be reported in voting (defaults: 1.0)
--maxDpConstraintSize: the number of subexons a constraint can cover in DP. (default: 7. -1 for inf)
--primaryParalog: use primary alignment to retain paralog genes (default: use unique alignments)
--version: print version and exit
--stage INT: (default: 0)
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