Created
April 13, 2013 19:48
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minor BasH5Reader change proposal
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Using the BasH5Reader is simple: | |
>>> b = BasH5Reader("m1122...bas.h5") # Load the file | |
>>> zmw = b[9] # Get Zmw object(s) by slicing on holenumber(s) | |
>>> myRead = zmw.subreads[0] # Get ZmwRead object | |
>>> myRead.basecalls() | |
"GATTACA" | |
>>> myRead.QualityValue() | |
array([5, 6, 3, 4, 8, 8, 1]) | |
My change proposal is to unify the naming of the ZmwRead accessors in | |
the Zmw class, and to provide the following principle: | |
* zmw.read, zmw.subReads, zmw.ccsRead are all HQ clipped; | |
* zmw[start:end] (and zmw[:]) is for the power user who may want to | |
go outside the HQ region. | |
Here is the change description: | |
| Old | New | Description | | |
|----------------+------------------------------+------------------------------------------| | |
| zmw.read() | zmw.read or zmw.unrolledRead | property returning entire read sequence, | | |
| | (decision needed) | clipped to the HQ region | | |
| | | | | |
| zmw.read(s, e) | zmw[s:e] | Access a custom subslice of the read. | | |
| | zmw[:] (to get everything) | This is the only way to get data from | | |
| | | outside the HQ region---intended for | | |
| | | power users. | | |
| | | | | |
| zmw.subreads | zmw.subReads | change name for consistency | | |
| | | | | |
| zmw.ccsRead | zmw.ccsRead | no change | | |
| | | | | |
| | | | |
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