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CmpH5Appendices.rst
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CmpH5Appendices.rst
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1. Example of a standard group layout
The following layout shows an example layout of a "cmp.h5" file for
in-house analysis. Some datasets are auxiliary for in-house data
analysis purposes. The summary for the exact set of datasets of the
different variants of 1.2.0 files is in section 18. (Note: The list
below is just an example not the full definition.)
::
/ Group
/AlnGroup Group
/AlnGroup/ID Dataset
/AlnGroup/Path Dataset
/AlnInfo Group
/AlnInfo/AlnIndex Dataset
/AlnInfo/Edna Dataset
/AlnInfo/ZScore Dataset
/FileLog Group
/FileLog/ID Dataset
/FileLog/Program Dataset
/FileLog/Version Dataset
/FileLog/Timestamp Dataset
/FileLog/CommandLine Dataset
/FileLog/Log Dataset
/MovieInfo Group
/MovieInfo/Exp Dataset
/MovieInfo/ID Dataset
/MovieInfo/Name Dataset
/MovieInfo/Run Dataset
/RefGroup Group
/RefGroup/ID Dataset
/RefGroup/Path Dataset
/RefGroup/RefGroupName Dataset
/RefGroup/RefInfoID Dataset
/RefInfo Group
/RefInfo/FullName Dataset
/RefInfo/ID Dataset
/RefInfo/Length Dataset
/RefInfo/MD5 Dataset
/ref000001 Group
/ref000001/m101005_050517_Jan_p1_b15 Group
/ref000001/m101005_050517_Jan_p1_b15/AlnArray Dataset
/ref000001/m101005_050517_Jan_p1_b15/IPD Dataset
/ref000001/m101005_050517_Jan_p1_b15/PulseWidth Dataset
/ref000001/m101005_050517_Jan_p1_b15/QualityValue Dataset
/ref000001/m101005_050517_Jan_p1_b15/StartTime Dataset
/ref000001/m101005_050517_Jan_p1_b15/pkmid Dataset
The following layout shows an example structure of a "cmp.h5" file
generated by a SpringField instrument. (Note: The list below is just
an example not the full definition.)
::
/ Group
/AlnGroup Group
/AlnGroup/ID Dataset
/AlnGroup/Path Dataset
/AlnInfo Group
/AlnInfo/AlnIndex Dataset
/FileLog Group
/FileLog/ID Dataset
/FileLog/Program Dataset
/FileLog/Version Dataset
/FileLog/Timestamp Dataset
/FileLog/CommandLine Dataset
/FileLog/Log Dataset
/MovieInfo Group
/MovieInfo/ID Dataset
/MovieInfo/Name Dataset
/MovieName Dataset
/RefGroup Group
/RefGroup/ID Dataset
/RefGroup/Path Dataset
/RefGroup/RefGroupName Dataset
/RefGroup/RefInfoID Dataset
/RefInfo Group
/RefInfo/FullName Dataset
/RefInfo/ID Dataset
/RefInfo/Length Dataset
/RefInfo/MD5 Dataset
/ref000001 Group
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0 Group
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0/AlnArray Dataset
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0/DeletionQV Dataset
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0/IPD Dataset
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0/InsertionQV Dataset
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0/PulseWidth Dataset
/ref000001/m101020_032930_terri_c000013271260000000115009501151151_s0_p0/QualityValue Dataset
/ref000001/m101020_043134_terri_c000013271260000000115009501151152_s0_p0/AlnArray Dataset
2. An example AlnIndex dataset
The following shows the first rows of an AlignmentIndex
DATASET "/AlnInfo/AlnIndex" {
DATATYPE H5T_STD_U32LE
DATASPACE SIMPLE { ( 310, 22 ) / ( H5S_UNLIMITED, 22 ) }
DATA {
(0,0): 220, 2, 1, 1, 0, 63, 0, 137, 1, 15, 0, 283, 348, 0, 63, 0,
2, 0,
(0,18): 116643, 116708, 0, 0,
(1,0): 173, 2, 1, 1, 0, 64, 0, 781, 1, 15, 0, 415, 483, 0, 63, 1,
4, 0,
(1,18): 79221, 79289, 1, 1,
(2,0): 216, 2, 1, 1, 0, 68, 0, 12, 1, 15, 0, 370, 443, 0, 68, 0,
5, 0,
(2,18): 115985, 116058, 2, 2,
(3,0): 250, 2, 1, 1, 0, 123, 0, 2094, 1, 15, 0, 155, 289, 0, 121,
0, 13,
(3,17): 2, 135141, 135277, 3, 3,
(4,0): 92, 2, 1, 1, 0, 143, 0, 2237, 1, 15, 0, 300, 449, 0, 139,
2, 8, 2,
(4,18): 17434, 17585, 4, 4,
(5,0): 200, 2, 1, 1, 0, 160, 0, 2734, 1, 15, 0, 273, 443, 0, 151,
4, 15,
(5,17): 5, 104018, 104193, 5, 5,
(6,0): 284, 2, 1, 1, 0, 186, 0, 1390, 1, 15, 0, 189, 381, 0, 181,
1, 10,
(6,17): 4, 162193, 162389, 6, 6,
(7,0): 274, 2, 1, 1, 0, 229, 0, 762, 1, 15, 0, 223, 476, 0, 223,
4, 26, 2,
(7,18): 153683, 153938, 7, 7,
(8,0): 237, 2, 1, 1, 0, 236, 0, 509, 1, 15, 0, 295, 558, 0, 231,
1, 31, 4,
(8,18): 129062, 129329, 8, 8,
(9,0): 214, 2, 1, 1, 0, 237, 0, 1291, 1, 15, 0, 455, 707, 0, 229,
4, 19,
(9,17): 4, 115013, 115269, 9, 9,
......
3. The following box shows an example of the standard
layout of a v. 1.2.0.SF file (without consensus data).
/ Group
/AlnGroup Group
/AlnGroup/ID Dataset {5/Inf}
/AlnGroup/Path Dataset {5/Inf}
/AlnInfo Group
/AlnInfo/AlnIndex Dataset {46605/Inf, 22}
/AlnInfo/ZScore Dataset {46605/Inf}
/FileLog Group
/FileLog/CommandLine Dataset {1/Inf}
/FileLog/ID Dataset {1/Inf}
/FileLog/Log Dataset {1/Inf}
/FileLog/Program Dataset {1/Inf}
/FileLog/Timestamp Dataset {1/Inf}
/FileLog/Version Dataset {1/Inf}
/MovieInfo Group
/MovieInfo/ID Dataset {5/Inf}
/MovieInfo/Name Dataset {5/Inf}
/RefGroup Group
/RefGroup/ID Dataset {1/Inf}
/RefGroup/Path Dataset {1/Inf}
/RefGroup/RefInfoID Dataset {1/Inf}
/RefInfo Group
/RefInfo/FullName Dataset {1/Inf}
/RefInfo/ID Dataset {1/Inf}
/RefInfo/Length Dataset {1/Inf}
/RefInfo/MD5 Dataset {1/Inf}
/ref000001 Group
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0
Group
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/AlnArray
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/DeletionQV
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/IPD
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/InsertionQV
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/PulseWidth
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/QualityValue
Dataset {4114996/Inf}
2. Example
The following group and dataset hierarchy shows
one example of a valid internal SAF HDF5 file
(attributes not shown, and without auxiliary
Zscore and EDNA datasets. )
/ Group
/AlnGroup Group
/AlnGroup/ID Dataset {5/Inf}
/AlnGroup/Path Dataset {5/Inf}
/AlnInfo Group
/AlnInfo/AlnIndex Dataset {46605/Inf, 22}
/AlnInfo/ZScore Dataset {46605/Inf}
/FileLog Group
/FileLog/CommandLine Dataset {1/Inf}
/FileLog/ID Dataset {1/Inf}
/FileLog/Log Dataset {1/Inf}
/FileLog/Program Dataset {1/Inf}
/FileLog/Timestamp Dataset {1/Inf}
/FileLog/Version Dataset {1/Inf}
/MovieInfo Group
/MovieInfo/Exp Dataset {5/Inf}
/MovieInfo/ID Dataset {5/Inf}
/MovieInfo/Name Dataset {5/Inf}
/MovieInfo/Run Dataset {5/Inf}
/RefGroup Group
/RefGroup/ID Dataset {1/Inf}
/RefGroup/Path Dataset {1/Inf}
/RefGroup/RefInfoID Dataset {1/Inf}
/RefInfo Group
/RefInfo/FullName Dataset {1/Inf}
/RefInfo/ID Dataset {1/Inf}
/RefInfo/Length Dataset {1/Inf}
/RefInfo/MD5 Dataset {1/Inf}
/ref000001 Group
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0
Group
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/AlnArray
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/DeletionQV
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/IPD
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/InsertionQV
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/PulseWidth
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/QualityValue
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/StartTime
Dataset {4114996/Inf}
/ref000001/m101207_232248_terri_c000024660070000000115022302181170_s1_p0/pkmid
Dataset {4114996/Inf}
``ConsensusCalls`` and ``ConsensusConfidence``
----------------------------------------------
.. warning::
The ``ConsensusCalls`` and ``ConsensusConfidence``
datasets are deprecated.
Post-mapping, the cmp.h5 may be consumed by an algorithm that produces
a consensus for a given reference. The consensus sequence and
corresponding P-values will be recorded in the .cmp.h5 file.
A ``Consensus`` group is defined under the reference group. Consensus
group contains two datasets, ConsensusCalls and ConsensusConfidence.
Consensus groups have several attributes, namely:
Algorithm Source - the name and version of the algorithm being used to
perform consensus calling
Sequence Sample Ploidy - whether the sample is haploid or diploid
Date Generated - time stamp for consensus calling results
ConsensusCalls is a single dimensional byte array that represents the
consensus call at each position with one byte. The compression
strategy is essentially the same as that used in the readBas-refBase
alignment, except that the first four bits are set by allele 1 and the
last four bits are set by the allele 2. If the sample was haploid,
then the first four bits would be untouched and the last four bits
would be set by the only allele present.
Byte Setting:
Diploid
Allele 1 Allele 2
------------------ ------------------
0 0 0 0 0 0 0 0
T G C A T G C A
Haploid
Allele
------------------
0 0 0 0 0 0 0 0
T G C A T G C A
ConsensusConfidence is a single dimensional float
array that stores the p-value associated with the
compressed call at each position. There is a 1:1
row correspondence between this dataset and the
ConsensusCalls dataset.
The explicit definition of HDF5 type for these two
datasets is shown below::
DATASET "/refSeq/Consensus/ConsensusCalls" {
DATATYPE H5T_STD_U8LE
DATASPACE SIMPLE { ( 100 ) / ( H5S_UNLIMITED ) }
}
DATASET "/refSeq/Consensus/ConsensusConfidence" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 100 ) / ( H5S_UNLIMITED ) }
}
Specification for the SAF used for Strobe Analysis
--------------------------------------------------
.. warning::
Strobe analyis is deprecated.
In addition to all datasets specified for the
standard SAF, the following additional datasets
are required for Strobe SAF files.
*FIXME: there is no file version for strobe?*
1. Within the info group ``MovieInfo``
- ``WhenStarted``: The relative time in seconds from hot start until
movie acquisition. This field is determined via the primary
"WhenStarted" field located in ``ScanData/AcqParams/`` from
bas.h5/pls.h5 by comparing ``WhenStarted`` to the time at which
the chip was put on the stage.
Data type and data space definition::
DATASET "/MovieInfo/MovieStartTime" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( * ) / ( H5S_UNLIMITED ) }
}
2. Within the info group ``AlnInfo`` containing information about each
alignment stored in the file
- ``StartTimeOffset``: a float32 dataset containing the StartTime
for the first aligned base.
Data type and data space definition::
DATASET "/AlnInfo/StartTimeOffset" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( * ) / ( H5S_UNLIMITED ) }
}
File layout specifications for previous `.cmp.h5` file format versions (pre 2.0)
==================================================================================
Version 1.2.0
-------------
+------------+------+-----------------+----------+-------+-----------+
|Parent Group| HDF5 |Resource Name |Data type | Shape | |
| | data | | | | |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |CommandLine |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Index |VLEN_STR |(3,) |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |ReadType |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Version |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |Path |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |DS |AlnIndex |uint32 | 22|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |CommandLine |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Log |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Program |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Timestamp |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Version |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |Name |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |AlnArray |uint8 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |OffsetTable |uint32 | 3|auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |Path |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |RefInfoID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |FullName |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |Length |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |MD5 |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |CommandLine |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Index |VLEN_STR |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |PrimaryPipeline |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |ReadType |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |ReportsFolder |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Version |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |Path |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |DS |AlnIndex |uint32 | 22|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |DS |Edna |float32 | 36|auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |DS |ZScore |float32 | 1|auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |CommandLine |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Log |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Program |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Timestamp |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Version |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |Exp |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |Name |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |Run |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |AlnArray |uint8 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |IPD |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |pkmid |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |PulseWidth |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |QualityValue |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |QualityValue |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |StartTime |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |OffsetTable |uint32 | 3|auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |Path |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |RefInfoID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |FullName |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |Length |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |MD5 |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |CommandLine |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Index |VLEN_STR |(3,) |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |ReadType |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Version |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |Path |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |DS |AlnIndex |uint32 | 22|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |CommandLine |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Log |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Program |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Timestamp |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Version |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |Name |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |AlnArray |uint8 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |DeletionQV |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |InsertionQV |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |IPD |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |PulseWidth |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |QualityValue |float32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |OffsetTable |uint32 | 3|auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |Path |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |RefInfoID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |MasterDataset |VLEN_STR |None |required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |nRow |uint32 |None |auxiliary |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |FullName |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |ID |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |Length |uint32 | 1|required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |MD5 |VLEN_STR | 1|required |
+------------+------+-----------------+----------+-------+-----------+
Version 1.3.1SF
---------------
+------------+------+-----------------+----------+-------+-----------+
|Parent Group| HDF5 |Resource Name |Data type | Shape| |
| | data | | | | |
+============+======+=================+==========+=======+===========+
|/ |ATTR |CommandLine |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Index |VLEN_STR | (3,)| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |ReadType |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/ |ATTR |Version |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |ID |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnGroup |DS |Path |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |DS |AlnIndex |uint32 | 22| required |
+------------+------+-----------------+----------+-------+-----------+
|/AlnInfo |ATTR |ColumnNames |VLEN_STR | 22| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |CommandLine |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |ID |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Log |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Program |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Timestamp |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/FileLog |DS |Version |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |ID |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |Name |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/MovieInfo |DS |FrameRate |float32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |AlnArray |uint8 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |QualityValue |uint8 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |DeletionQV |uint8 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |InsertionQV |uint8 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |MergeQV |uint8 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |SubstitutionQV |uint8 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |SubstitutionTag |char | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |DeletionTag |char | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |IPD |uint16 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |PulseWidth |uint16 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/ref*/* |DS |PulseIndex |uint32 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |ID |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |OffsetTable |uint32 | 3| optional |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |Path |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefGroup |DS |RefInfoID |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |ATTR |MasterDataset |VLEN_STR | None| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |FullName |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |ID |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |Length |uint32 | 1| required |
+------------+------+-----------------+----------+-------+-----------+
|/RefInfo |DS |MD5 |VLEN_STR | 1| required |
+------------+------+-----------------+----------+-------+-----------+
**Additional datasets available in Version 1.3.1.PB:**
+------------+------+-----------------+----------+-------+-----------+
|Parent Group| HDF5 |Resource Name |Data type | Shape| |
| | data | | | | |
+============+======+=================+==========+=======+===========+
|/ref*/* |DS |StartFrame |uint32 | 1| optional |
+------------+------+-----------------+----------+-------+-----------+