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LoadVariants Header Format #1815

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Georgehe4 opened this issue Dec 3, 2017 · 1 comment
Closed

LoadVariants Header Format #1815

Georgehe4 opened this issue Dec 3, 2017 · 1 comment
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@Georgehe4
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@Georgehe4 Georgehe4 commented Dec 3, 2017

I am trying to load a variant file but have been having issues with the header format -- any suggestions?

IllegalArgumentExceptionTraceback (most recent call last)
<ipython-input-14-f4a5abfe2012> in <module>()
      1 # Variants
----> 2 variants = ac.loadVariants(variantFile)

/opt/cgl-docker-lib/mango/mango-python/adam/adam-python/bdgenomics/adam/adamContext.pyc in loadVariants(self, filePath, stringency)
    212 
    213         adamRdd = self.__jac.loadVariants(filePath,
--> 214                                           _toJava(stringency, self._jvm))
    215 
    216         return VariantRDD(adamRdd, self._sc)

/usr/lib/spark/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py in __call__(self, *args)
   1131         answer = self.gateway_client.send_command(command)
   1132         return_value = get_return_value(
-> 1133             answer, self.gateway_client, self.target_id, self.name)
   1134 
   1135         for temp_arg in temp_args:

/usr/lib/spark/python/pyspark/sql/utils.pyc in deco(*a, **kw)
     77                 raise QueryExecutionException(s.split(': ', 1)[1], stackTrace)
     78             if s.startswith('java.lang.IllegalArgumentException: '):
---> 79                 raise IllegalArgumentException(s.split(': ', 1)[1], stackTrace)
     80             raise
     81     return deco

IllegalArgumentException: u'Field type for provided header line (FORMAT=<ID=MQ,Number=1,Type=Integer,Description="RMS Mapping Quality">) does not match supported line (FORMAT=<ID=MQ,Number=1,Type=Float,Description="Root mean square (RMS) mapping quality">)'
@Georgehe4 Georgehe4 changed the title LoadVariant Header Format LoadVariants Header Format Dec 3, 2017
@fnothaft
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@fnothaft fnothaft commented Dec 3, 2017

You should be able to bypass any validation errors with:

from bdgenomics.adam.adamContext import ADAMContext
from bdgenomics.adam.stringency import LENIENT

ac = ADAMContext(sc)
variants = ac.loadVariants(variantFile, stringency=LENIENT)
@Georgehe4 Georgehe4 closed this Dec 4, 2017
@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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