Resequencing Condition Type

ResequencingConditionType.md

Resequencing Condition Type

Has both the SubreadSet, ReferenceSet and final AlignmentSet output

{
  "_condition_doc": "Example of a 'Resequencing' Condition Type",
  "conditions": [
    {
      "condId": "cond_alpha",
      "subreadset": "/path/to/subreadset-01.xml",
      "alignmentset": "/path/to/alignmentset-A.xml",
      "referenceset": "/path/to/reference.xml"
    },
    {
      "condId": "cond_alpha",
      "subreadset": "/path/to/subreadset-02.xml",
      "alignmentset": "/path/to/alignmentset-B.xml",
      "referenceset": "/path/to/reference.xml"
    },
    {
      "condId": "cond_beta",
      "subreadset": "/path/to/subreadset-03.xml",
      "alignmentset": "/path/to/alignmentset-C.xml",
      "referenceset": "/path/to/reference.xml"
    },
  ],
  "pipelineId": "pbsmrtpipe.pipelines.my_pipeline"
}

Future condition types, such as, Reseq CCS Condition type, would have Consensus AlignmentSet instead of alignmentset.

{
  "_condition_doc": "Example of a 'Resequencing CCS' Condition Type",
  "conditions": [
    {
      "condId": "cond_alpha",
      "subreadset": "/path/to/subreadset-01.xml",
      "ccsalignmentset": "/path/to/consensus-alignmentset-A.xml",
      "referenceset": "/path/to/reference.xml"
    },
    {
      "condId": "cond_alpha",
      "subreadset": "/path/to/subreadset-02.xml",
      "ccsalignmentset": "/path/to/consensus-B.xml",
      "referenceset": "/path/to/reference.xml"
    },
    {
      "condId": "cond_beta",
      "subreadset": "/path/to/subreadset-03.xml",
      "ccsalignmentset": "/path/to/consensus-C.xml",
      "referenceset": "/path/to/reference.xml"
    },
  ],
  "pipelineId": "pbsmrtpipe.pipelines.my_pipeline"
}