###Header
| Field | Description | Type | Value |
|---|---|---|---|
| Magic | HiC magic string | String | HIC |
| Version | Version number | int | 8 |
| mIdxPos | File position of master index | ||
| genomeId | Genome identifier (e.g. hg19, mm9, etc) | String | |
| nAttributes | Number of key-value pair attributes | int | |
| List of key-value pair attributes (n = nAttributes) | |||
| key | String | ||
| value | String | ||
| nChrs | Number of chromosomes | int | |
| List of chromosome lengths (n = nChrs) | |||
| chrName | Chromosome name | String | |
| chrLength | Chromosome length | int | |
| nBpResolutions | Number of base pair resolutions | int | |
| List of bin sizes for bp resolution levels (n = nBpResolutions) | |||
| resBP | Bin size in base pairs | int | |
| nFragResolutions | Number of fragment resolutions | int | |
| List of bin sizes for frag resolution levels (n = nFragResolutions) | |||
| resFrag | Bin size in fragment units (1, 2, 5, etc) | int | |
| List of fragment sites per chromosome, in same order as chromosome list above (n = nChrs). This section absent if nFragResolutions == 0.) | |||
| nSites | Number of sites for this chromosome | int | |
| List of sites (n = nSites) | |||
| site | Site position in base pairs | int |
###Body
| Field | Description | Type | Value |
|---|---|---|---|
| The section below is repeated for each chr-chr combination | |||
| chr1Idx | Chr 1 index | int | |
| chr2Idx | Chr 2 index | int | |
| nResolutions | Total number of resolutions, including base pair and fragment resolutions. | int | |
| Resolution headers (n = nResolutions) | |||
| unit | Distance unit, base-pairs or fragments | String | FRAG : BP |
| resIdx | Index number for this resolution level. | int | |
| sumCounts | Sum of all counts (or scores) across all bins | float | |
| occupiedCellCount | Total count of cells that are occupied | int | |
| percent90 | Estimate of 90th percentile of counts among occupied bins | ||
| percent95 | Estimate of 95th percentile of counts among occupied bins | ||
| binSize | The bin size in base-pairs or fragments | ||
| blockBinCount | |||
| blockColumnCount | |||
| blockCount | |||
| Block index (n = nResolutions) | |||
| blockID | Numeric id for block | int | |
| blockPosition | File position of block | long | |
| blockSize | Size of block in bytes | ||
| Resolution level data (n = nResolutions) | |||
| Block data (n = blockCount) | |||
| cellCount | Number or cells in this block (sparse matrix) | int | |
| Cell data (n = cellCount) | |||
| binX | X axis index | int | |
| binY | Y axis index | long | |
| value | Value (counts or score) | float |
###Footer
| Field | Description | Type | Value |
|---|---|---|---|
| nBytesV5 | Number of bytes for the “v5” footer, that is everything up to the normalized expected vectors | int | |
| Master index for “Matrix” records | |||
| nEntries | Number of index entries | int | |
| List of index entries (n = nEntries) | |||
| key | Key, constructed as _ | String | |
| position | Position of start of matrix record in bytes | long | |
| size | Size of matrix record in bytes | int | |
| Expected value vectors | |||
| nExpectedValueVectors | Number of expected value vectors to follow. These are expected values from the non-normalized observed matrix. | int | |
| List of expected value vectors (n = nExpectedValueVectors) | |||
| binSize | Bin (grid) size for this calculation | int | |
| unit | Bin units either FRAG or BP. | String | FRAG : BP |
| nValues | Size of the vector | int | |
| List of expected values (n = nValues) | |||
| value | Expected value | double | |
| nChrScaleFactors | |||
| List of normalization factors (n = nChrScaleFactors) | |||
| chrIndex | Chromosome index | int | |
| chrScaleFactor | Chromosome scale factor | double | |
| nNormExpectedValueVectors | Number of normalized expected value vectors to follow | int | |
| Type | Indicates type of normalization | String | VC:KR:INTER_KR:INTER_VC:GW_KR:GW_VC |
| binSize | Bin (grid) size for this calculation | int | |
| unit | Bin units either FRAG or BP. | String | FRAG : BP |
| nValues | Size of the vector | int | |
| List of expected values (n = nValues) | |||
| value | Expected value | double | |
| nChrScaleFactors | |||
| List of normalization factors (n = nChrScaleFactors) | |||
| chrIndex | Chromosome index | int | |
| chrScaleFactor | Chromosome scale factor | double | |
| Normalization vector index | |||
| nNormVectors | Number of normalization vectors | int | |
| List of normalization vectors (n= nNormalizationVectors) | |||
| type | Indicates type of normalization | String | VC:KR:INTER_KR:INTER_VC:GW_KR:GW_VC |
| chrIdx | Chromosome index | int | |
| unit | Bin units either FRAG or BP. | String | FRAG : BP |
| binSize | Resolution | int | |
| position | File position of value array | long | |
| nBytes | Size in bytes of value array | int | |
| Normalization vector arrays (repeat for each entry above) | |||
| nValues | Number of values in array | int | |
| Normalization vector values (n= nValues) | |||
| value | double | ||
| Attribute dictionary | |||
| nAttributes | Number of attributes | int | |
| List of key-value pair attributes (n = nAttributes) | |||
| key | String | ||
| value | String |