Justin Paschall
Justin Paschall
When I attempt to install from Master as below, I get the following error: ``` git clone [email protected]:bigdatagenomics/mango.git virtualenv venv source venv/bin/activate cd mango/mango-viz/ make prepare cd ../mango-python/ make prepare...
I want to try Mango with the ADAM Hive partitioning PR: https://github.com/bigdatagenomics/adam/pull/1620 This is going to require some more changes than just bumping scala and spark versions, error I get...
Looking at the String that is the first element in the Value 2-tuple in: ``` var intRDD: IntervalRDD[ReferenceRegion, (String, T)] = null ``` https://github.com/bigdatagenomics/mango/blob/master/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala#L64 This String appears to be always...
Wanted to point to my current dev branch: https://github.com/jpdna/mango/tree/ga4gh6 New features: Endpoints - /ga4gh/variants/search/bin - /ga4gh/variants/search The GA4GH bin endpoint returns counts of variants in the bin The GA4GH /varaints/search...
In ADAM/Mango a genotype call is defined as a list of `GenotypeAllele` here: https://github.com/bigdatagenomics/bdg-formats/blob/master/src/main/resources/avro/bdg.avdl#L966 `GenotypeAllele` is defined as one of: https://github.com/bigdatagenomics/bdg-formats/blob/master/src/main/resources/avro/bdg.avdl#L753 In cases where a multi-allelic variant was split (as...
I'm getting a weird overridden method compile type incompatibility error ``` [ERROR] /home/paschalj/mango8/mango/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterializationGA4GH.scala:104: error: overriding method stringify in class LazyMaterialization of type (rdd: org.apache.spark.rdd.RDD[(String, ga4gh.Variants.Variant)])Map[String,String]; [ERROR] method stringify has incompatible...
I want to use the GA4GH schema protobuf generated java classes for purposes of enabling Mango/bdgenomics GA4GH services. Until the Maven objects are available at Maven Central, I want to...
Using Mango as of 9f518e0 I created test input data based on the ChrM mouse files using ADAM. I launch Mango with: ``` ./bin/mango-submit data/test_files/mm10_chrM.fa -read_files data/test_files/mouse_chrM_adam.adam -var_files data/test_files/small_adam_vcf.adam -feat_file...
#I'm trying to generate code from the GA4GH-schema proto files using: https://github.com/square/wire At the moment I am chasing down file dependencies as maven is telling me: ``` Wire Plugin: Failure...
Hi, GEMINI is a great tool! We'd like to use and possibly extend the web-browser for local needs. I have a gemini database that works fine for `gemini query` command...