hammerlab/guacamole — pull request #101 by tavinathanson (2014-06-11 22:40:12+00:00)
Title: Pretty print to stdout when the -out argument is not passed in

Let me know if this is what you had in mind. Example output (spacing not shown in the comment):

} {
"variant" : {
"org.bdgenomics.adam.avro.ADAMVariant" : {
"contig" : {
"org.bdgenomics.adam.avro.ADAMContig" : {
"contigName" : {
"string" : "chrM"
},
"contigLength" : null,
"contigMD5" : null,
"referenceURL" : null
}
},
"position" : {
"long" : 16321
},
"referenceAllele" : "T",
"variantAllele" : "C"
}
},
"variantCallingAnnotations" : null,
"sampleId" : {
"string" : "default"
},
"sampleDescription" : null,
"processingDescription" : null,
"alleles" : [ "Alt", "Alt" ],
"referenceReadDepth" : null,
"alternateReadDepth" : null,
"readDepth" : null,
"genotypeQuality" : null,
"genotypeLikelihoods" : [ ],
"expectedAlleleDosage" : null,
"readsMappedForwardStrand" : null,
"splitFromMultiAllelic" : false,
"isPhased" : null,
"phaseSetId" : null,
"phaseQuality" : null
} {