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heuermh

Ensembl Variant Effect Predictor annotations support

3

I have already been using Adam with snpEff annotations and it worked great. However, when I've tried to use it with a VCF file annotated using Ensembl VEP it didn't...

znikasz

StackOverflowError in avro SpecificDatumWriter

1

``` $ spark-submit --version Welcome to ____ __ / __/__ ___ _____/ /__ _\ \/ _ \/ _ `/ __/ '_/ /___/ .__/\_,_/_/ /_/\_\ version 3.2.0 /_/ Using Scala version...

heuermh

Bump htsjdk dependency version to 2.20.3

8

Expected to fail CI.

heuermh

heuermh

Inconsistent counts for shuffleRegionJoin without Sequence Dictionaries

3

Shuffle region join between two GFF3 files, downloaded from ftp://ftp.ensembl.org/pub/release-91/gff3/homo_sapiens/ and ftp://ftp.ensembl.org/pub/release-91/regulation/homo_sapiens/, read from HDFS with and without providing a sequence dictionary: ``` $ adam-shell ... scala> import org.bdgenomics.adam.rdd.ADAMContext._ import...

heuermh

Added an optimisation to spare not required shuffle of unpaired reads

27

This PR adds an option to avoid shuffling the entire alignment dataset when transforming to FragmentDataset. This adds a boolean parameter to the function toFragments() that, when specified, the FragmentDataset...

benraha

Spare not needed groupBy when calling toFragments() on AlignmentDataset

4

Hi! I'm running a process that is pre-processing a bunch of reads before aligning them using Bowtie. Most of them are unpaired, so when I run toFragments(), I need to...

benraha

I'm failing to use this package

11

Hi, I try to install this package and use it but I'm constantly failing. What I did so far: 1) set up Anaconda with PySpark 2.4.4 2) `pip install bdgenomics.adam`...

Hoeze

TypeError: 'JavaPackage' object is not callable

13

Python: When I am trying to run `ADAMContext(sparkSession)` , I am getting this error: ``` c = self._jvm.org.bdgenomics.adam.rdd.ADAMContext.ADAMContextFromSession(ss._jsparkSession) TypeError: 'JavaPackage' object is not callable ``` The full code I am...

Shekharrajak