NEWS

knowYourCG 1.9.4

bedToCg: the bedtools/yame pipeline reached sh -c unquoted, so sh ran a bare 'yame' and the output file was empty. It is now quoted.
testEnrichment2: the odds ratio is computed in double precision. Integer counts from YAME overflowed on genome-scale tables and gave NA estimates.
testEnrichment2: an unmeetable min_overlap returns the empty result without a second warning.
KYCG_plotEnrichAll: geom_segment(linewidth=), not the deprecated size=.

testEnrichmentSEA: the two tails now share one pooled permutation null, so the p-value no longer depends on the sign of the query (zhou-lab/knowYourCG#6)
testEnrichmentSEA: the sign of estimate is flipped to match GSEA. Positive now means the set is enriched at large values, negative at small values. Results from earlier versions have the opposite sign. KYCG_plotSetEnrichment now walks from the largest value down.