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"
]
}