pbindexdump

Usage: pbindexdump [options] [input]

pbindexdump prints a human-readable view of PBI data to stdout.

Options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

Input/Output:
  input               Input PBI file. If not provided, stdin will be used as input.
  --format=STRING     Output format, one of:
                          json, cpp

                      json: pretty-printed JSON [default]

                      cpp: copy/paste-able C++ code that can be used to
                      construct the equivalent PacBio::BAM::PbiRawData object

JSON Formatting:
  --json-indent-level=INT
                      JSON indent level [4]
  --json-raw          Prints fields in a manner that more closely reflects the
                      PBI file format - presenting data as per-field columns,
                      not per-record objects.

JSON Output Schemas

Normal JSON:

{
  "type": "object",
  "properties": {
    "fileSections": {
      "type": "array",
      "items": { "type": "string" },
    },
    "numReads": { "type": "integer" },
    "reads": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "aEnd": { "type": "integer" },
          "aStart": { "type": "integer" },
          "bcForward": { "type": "integer" },
          "bcQuality": { "type": "integer" },
          "bcReverse": { "type": "integer" },
          "contextFlag": { "type": "integer" },
          "fileOffset": { "type": "integer" },
          "holeNumber": { "type": "integer" },
          "mapQuality": { "type": "integer" },
          "nM": { "type": "integer" },
          "nMM": { "type": "integer" },
          "qEnd": { "type": "integer" },
          "qStart": { "type": "integer" },
          "readQuality": { "type": "number" },
          "reverseStrand": { "type": "integer" },
          "rgId": { "type": "integer" },
          "tEnd": { "type": "integer" },
          "tId": { "type": "integer" },
          "tStart: { "type": "integer" }
        },
        "required": [
          "contextFlag",
          "fileOffset",
          "holeNumber",
          "qEnd",
          "qStart",
          "readQuality",
          "rgId"
        ]
      }
    },
    "references": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "beginRow": { "type": "integer" },
          "endRow": { "type": "integer" },
          "tId": { "type": "integer" }
        },
        "required" : [ "beginRow", "endRow","tId" ]
      }
    }q
    "version": { "type": "string" }
  },
  "required": [
    "fileSections",
    "numReads",
    "reads",
    "version"
  ]
}

“Raw” JSON:

{
  "type": "object",
  "properties": {
    "barcodeData" : {
      "type" : "object",
      "properties: {
        "bcForward" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "bcQuality" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "bcReverse" : {
          "type": "array",
          "items" : { "type": "integer" }
        }
      }
    },
    "basicData" : {
      "type" : "object",
      "properties: {
        "contextFlag" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "fileOffset" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "holeNumber" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "qEnd" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "qStart" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "readQuality" : {
          "type": "array",
          "items" : { "type": "number" }
        },
        "rgId : {
          "type": "array",
          "items" : { "type": "integer" }
        }
      }
    },
    "fileSections": {
      "type": "array",
      "items": { "type": "string" },
    },
    "mappedData" : {
      "type" : "object",
      "properties: {
        "aEnd" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "aStart" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "mapQuality" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "nM" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "nMM" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "readQuality" : {
          "type": "array",
          "items" : { "type": "number" }
        },
        "reverseStrand" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "tEnd" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "tId" : {
          "type": "array",
          "items" : { "type": "integer" }
        },
        "tStart" : {
          "type": "array",
          "items" : { "type": "integer" }
        }
      }
    },
    "numReads": { "type": "integer" },
    "references": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "beginRow": { "type": "integer" },
          "endRow": { "type": "integer" },
          "tId": { "type": "integer" }
        },
        "required" : [ "beginRow", "endRow","tId" ]
      }
    },
    "version" : { "type": "string" }
  },
  "required": [
    "fileSections",
    "numReads",
    "basicData",
    "version"
  ]
}