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mdozmorov / genome_runner

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Annotation analysis bug #31

Closed mdozmorov closed 10 years ago

mdozmorov commented 10 years ago

columns in the annotation file do not match actual annotations. E.g., there may be 43 out of 60 SNPs enriched in a GF, but annotation column with 43 SNPs marked as overlapping this GF is misplaced.

Details to reproduce: https://gist.github.com/mdozmorov/cd77e983042c0f8ea3e4

It may be easier to show on screen

mdozmorov commented 10 years ago

Misplaced columns are actually in reverse of the actual call: annotationAnalysis evofold.bed evofold.bed.gz | head Region /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/genes/evofold.bed.gz chr1|78193664|78193665 0 chr1|90915479|90915480 0 chr1|108024415|108024416 1 chr1|198264631|198264632 1 chr1|204976076|204976077 0

annotationAnalysis evofold.bed evofold.bed.gz knownGene.bed.gz | head Region /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/genes/evofold.bed.gz /home/dozmorovm/db_1.00_06.10.2014/grsnp_db/hg19/genes/knownGene.bed.gz chr1|78193664|78193665 5 0 chr1|90915479|90915480 0 0 chr1|108024415|108024416 9 1 chr1|198264631|198264632 2 1 chr1|204976076|204976077 8 0 chr1|210970904|210970905 2 1

annotationAnalysis evofold.bed evofold.bed.gz knownGene.bed.gz wgRna.bed.gz exoniphy.bed.gz | head Region ... chr1|78193664|78193665 0 0 5 0 chr1|90915479|90915480 0 0 0 0 chr1|108024415|108024416 0 0 9 1 chr1|198264631|198264632 1 0 2 1 chr1|204976076|204976077 0 0 8 0 chr1|210970904|210970905 1 0 2 1

lkscara commented 10 years ago

Fixed in 225896d