===========================
Revio & Vega file structure
===========================

The Revio and Vega platforms have a different output file structure than Sequel
II and Sequel IIe.

Directory structure
===================

.. code-block::

   Transfer_Scheme_Path/
   └─ rNNNNN_YYYYMMDD_HHMMSS/
      └─ P_WNN/
         ├─ fail_reads/
         ├─ hifi_reads/
         ├─ metadata/
         ├─ pb_formats/
         └─ statistics/

Movie Context ID is defined as

.. code-block::

   mNNNNN_YYMMDD_HHMMSS_sN

in particular::

   mNNNNN - instrument identifier
   YYMMDD - date stamp
   HHMMSS - time stamp
   sN     - stage number (Revio has four)

File structure
==============

Barcoded data example (from Revio)
----------------------------------

In the following example, one barcode ('bc2001') has been used. If
you see the 'default' file infix, this is the standard, unbarcoded TC6 SMRTbell
adapter.

.. code-block::

   Transfer_Scheme_Path/
   └─r84001_20220722_134701
     └─1_A01
       ├─ fail_reads
       │  ├─ m84001_220722_134701_s1.fail_reads.bc2001.bam
       │  ├─ m84001_220722_134701_s1.fail_reads.bc2001.bam.pbi
       │  ├─ m84001_220722_134701_s1.fail_reads.unassigned.bam
       │  └─ m84001_220722_134701_s1.fail_reads.unassigned.bam.pbi
       ├─ hifi_reads
       │  ├─ m84001_220722_134701_s1.hifi_reads.bc2001.bam
       │  ├─ m84001_220722_134701_s1.hifi_reads.bc2001.bam.pbi
       │  ├─ m84001_220722_134701_s1.hifi_reads.unassigned.bam
       │  └─ m84001_220722_134701_s1.hifi_reads.unassigned.bam.pbi
       ├─ metadata
       │  ├─ m84001_220722_134701_s1.barcodes.fasta
       │  ├─ m84001_220722_134701_s1.basecaller.log
       │  ├─ m84001_220722_134701_s1.ccs.log
       │  ├─ m84001_220722_134701_s1.darkcal.log
       │  ├─ m84001_220722_134701_s1.fail_reads.alarms.json
       │  ├─ m84001_220722_134701_s1.fail_reads.lima.log
       │  ├─ m84001_220722_134701_s1.fail_reads.primrose.log
       │  ├─ m84001_220722_134701_s1.hifi_reads.alarms.json
       │  ├─ m84001_220722_134701_s1.hifi_reads.lima.log
       │  ├─ m84001_220722_134701_s1.hifi_reads.primrose.log
       │  ├─ m84001_220722_134701_s1.metadata.xml
       │  ├─ m84001_220722_134701_s1.ppa.log
       │  ├─ m84001_220722_134701_s1.run.metadata.xml
       │  ├─ m84001_220722_134701_s1.sts.xml
       │  └─ m84001_220722_134701_s1.transferdone
       ├─ pb_formats
       │  ├─ m84001_220722_134701_s1.consensusreadset.xml
       │  ├─ m84001_220722_134701_s1.fail_reads.bc2001.consensusreadset.xml
       │  ├─ m84001_220722_134701_s1.fail_reads.consensusreadset.xml
       │  ├─ m84001_220722_134701_s1.fail_reads.unassigned.consensusreadset.xml
       │  ├─ m84001_220722_134701_s1.hifi_reads.bc2001.consensusreadset.xml
       │  ├─ m84001_220722_134701_s1.hifi_reads.consensusreadset.xml
       │  └─ m84001_220722_134701_s1.hifi_reads.unassigned.consensusreadset.xml
       └─ statistics
          ├─ m84001_220722_134701_s1.ccs_reports.json
          ├─ m84001_220722_134701_s1.fail_reads.5mc_report.json
          ├─ m84001_220722_134701_s1.fail_reads.lima_counts.txt
          ├─ m84001_220722_134701_s1.fail_reads.lima_guess.json
          ├─ m84001_220722_134701_s1.fail_reads.lima_report.txt
          ├─ m84001_220722_134701_s1.fail_reads.lima_summary.txt
          ├─ m84001_220722_134701_s1.hifi_reads.5mc_report.json
          ├─ m84001_220722_134701_s1.hifi_reads.lima_counts.txt
          ├─ m84001_220722_134701_s1.hifi_reads.lima_guess.json
          ├─ m84001_220722_134701_s1.hifi_reads.lima_report.txt
          ├─ m84001_220722_134701_s1.hifi_reads.lima_summary.txt
          └─ m84001_220722_134701_s1.zmw_metrics.json.gz


Non-barcoded data example (from Vega)
-------------------------------------

.. code-block::

  Transfer_Scheme_Path/
  └─r21012_20241030_183049
    └─1_A01
      ├─ fail_reads
      |  ├─ m21012_241030_210509.fail_reads.bam
      │  └─ m21012_241030_210509.fail_reads.bam.pbi
      ├─ hifi_reads
      │  ├─ m21012_241030_210509.hifi_reads.bam
      │  └─ m21012_241030_210509.hifi_reads.bam.pbi
      ├─ metadata
      │  ├─ m21012_241030_210509.basecaller.log
      │  ├─ m21012_241030_210509.baz2bam.log
      │  ├─ m21012_241030_210509.ccs.log
      │  ├─ m21012_241030_210509.combined_baz2bam.log
      │  ├─ m21012_241030_210509.fail_reads.jasmine.log
      │  ├─ m21012_241030_210509.fail_reads.samtools.log
      │  ├─ m21012_241030_210509.fail_reads.trim.log
      │  ├─ m21012_241030_210509.finalize-dataset.log
      │  ├─ m21012_241030_210509.hifi_reads.jasmine.log
      │  ├─ m21012_241030_210509.hifi_reads.samtools.log
      │  ├─ m21012_241030_210509.hifi_reads.trim.log
      │  ├─ m21012_241030_210509.metadata.xml
      │  ├─ m21012_241030_210509.sts.xml
      │  ├─ m21012_241030_210509.transferdone
      │  └─ m21012_241030_210509.transferfail
      ├─ pb_formats
      │  └─ m21012_241030_210509.hifi_reads.consensusreadset.xml
      └─ statistics
         ├─ m21012_241030_210509.ccs_report.json
         ├─ m21012_241030_210509.ccs_report.txt
         ├─ m21012_241030_210509.fail_reads.5mc_report.json
         ├─ m21012_241030_210509.hifi_reads.5mc_report.json
         ├─ m21012_241030_210509.pbreports.log
         ├─ m21012_241030_210509.report.pdf
         ├─ m21012_241030_210509.reports.zip
         ├─ m21012_241030_210509.summary.json
         ├─ m21012_241030_210509.zmw_metrics.csv.gz
         └─ m21012_241030_210509.zmw_metrics.json.gz