search

chapmanb / bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure
66 stars 15 forks source link

File duplicates returned by API #7

Closed lynaghk closed 12 years ago

lynaghk commented 12 years ago

The bcbio.variation.api.file/get-files method is serving up duplicate entries:

({:id "gs:/Home/keminglabs/test/freebayes-calls.vcf", :tags ("test"), :folder "/Home/keminglabs/test", :filename "freebayes-calls.vcf"} {:id "gs:/Home/keminglabs/test/gatk-calls.vcf", :tags ("test"), :folder "/Home/keminglabs/test", :filename "gatk-calls.vcf"} {:id "gs:/Home/keminglabs/test/filter/freebayes-calls-filter.vcf", :tags ("test/filter"), :folder "/Home/keminglabs/test/filter", :filename "freebayes-calls-filter.vcf"} {:id "gs:/Home/keminglabs/test/filter/gatk-calls-filter.vcf", :tags ("test/filter"), :folder "/Home/keminglabs/test/filter", :filename "gatk-calls-filter.vcf"} {:id "gs:/Home/keminglabs/test/freebayes-calls.vcf", :tags ("test"), :folder "/Home/keminglabs/test", :filename "freebayes-calls.vcf"} {:id "gs:/Home/keminglabs/test/gatk-calls.vcf", :tags ("test"), :folder "/Home/keminglabs/test", :filename "gatk-calls.vcf"} {:id "gs:/Home/keminglabs/test/filter/freebayes-calls-filter.vcf", :tags ("test/filter"), :folder "/Home/keminglabs/test/filter", :filename "freebayes-calls-filter.vcf"} {:id "gs:/Home/keminglabs/test/filter/gatk-calls-filter.vcf", :tags ("test/filter"), :folder "/Home/keminglabs/test/filter", :filename "gatk-calls-filter.vcf"})

Restarting lein doesn't fix the issue. The server tmp directory matches up with genomespace: both only have four files total (gatk and freebayes and their filtered variants).