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Slow5Reader.html
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<main>
<article id="content">
<header>
<h1 class="title">Module <code>read5.Slow5Reader</code></h1>
</header>
<section id="section-intro">
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">#!/usr/bin/env python
# author: Jannes Spangenberg
# e-mail: jannes.spangenberg@uni-jena.de
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
from read5.AbstractFileReader import AbstractFileReader
import pyslow5
import numpy as np
class Slow5Reader(AbstractFileReader):
'''
File reader for slow5 or blow5 files
Attributes
----------
threads : int
number of threads to use in C backend
batchsize : int
number of reads to fetch at a time. Higher numbers use more ram, but is more efficient with more threads.
filepath : str
Path to the ONT raw data file
Raises
------
FileNotFoundError
If the given file does not exist.
'''
def __init__(self, threads : int = 1, batchsize : int = 1, *args, **kwargs):
self._threads = threads
self._batchsize = batchsize
super().__init__(*args, **kwargs)
def open(self) -> None:
self._file = pyslow5.Open(self._filepath, 'r')
if self._threads > 1:
self._reads = self._file.seq_reads_multi(threads=self._threads, batchsize=self._batchsize)
else:
self._reads, self._nreads = self._file.get_read_ids()
self._open = True
def __getitem__(self, readid : str):
return self._file.get_read(readid)
def getSignal(self, readid : str) -> np.ndarray:
return self.__getitem__(readid)['signal']
def getOffset(self, readid : str) -> float:
return self.__getitem__(readid)['offset']
def getRange(self, readid : str) -> float:
return self.__getitem__(readid)['range']
def getDigitisation(self, readid : str) -> int:
return self.__getitem__(readid)['digitisation']
def getCalibrationScale(self, readid : str) -> float:
return self.getRange(readid) / self.getDigitisation(readid)
def getpASignal(self, readid :str) -> np.ndarray:
return self._file.get_read(readid, pA=True)['signal']
def getChannelNumber(self, readid : str) -> int:
return int(self._file.get_read(readid, aux='channel_number')['channel_number'])
def getStartTime(self, readid : str) -> int:
return self._file.get_read(readid, aux='start_time')['start_time']
def getReadNumber(self, readid : str) -> int:
return self._file.get_read(readid, aux='read_number')['read_number']
def getMedianBefore(self, readid : str) -> int:
return self._file.get_read(readid, aux='median_before')['median_before']
def getStartMux(self, readid : str) -> int:
'''
Returns
-------
start_mux : int
'''
return self._file.get_read(readid, aux='start_mux')['start_mux']
def getEndReason(self, readid : str) -> int:
return self._file.get_read(readid, aux='end_reason')['end_reason']
def getDuration(self, readid : str) -> int:
return self.__getitem__(readid)['len_raw_signal']
def getSamplingRate(self, readid : str) -> int:
return self.__getitem__(readid)['sampling_rate']
### get_all_headers
def getAllHeaders(self) -> dict:
'''
Returns
-------
metadata : dict
all metadata of the sequencing run stored in file.get_all_headers()
'''
return self._file.get_all_headers()
def getAsicID(self, readid : str = None) -> str:
return self.getAllHeaders()['asic_id']
def getAsicIDEeprom(self, readid : str = None) -> str:
return self.getAllHeaders()['asic_id_eeprom']
def getAsicTemp(self, readid : str = None) -> float:
return float(self.getAllHeaders()['asic_temp'])
def getAsicVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['asic_version']
def isAutoUpdated(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['auto_update']))
def getAutoUpdateSource(self, readid : str = None) -> str:
return self.getAllHeaders()['auto_update_source']
def isBarcodingEnabled(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['barcoding_enabled']))
def isBreamStandard(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['bream_is_standard']))
def getConfigurationVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['configuration_version']
def getDeviceID(self, readid : str = None) -> str:
return self.getAllHeaders()['device_id']
def getDeviceType(self, readid : str = None) -> str:
return self.getAllHeaders()['device_type']
def getDistributionStatus(self, readid : str = None) -> str:
return self.getAllHeaders()['distribution_status']
def getDistributionVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['distribution_version']
def getExpScriptName(self, readid : str = None) -> str:
return self.getAllHeaders()['exp_script_name']
def getExpScriptPurpose(self, readid : str = None) -> str:
return self.getAllHeaders()['exp_script_purpose']
def getExpStartTime(self, readid : str = None) -> str:
return self.getAllHeaders()['exp_start_time']
def getExperimentDurationSet(self, readid : str = None) -> int:
return int(self.getAllHeaders()['experiment_duration_set'])
def getExperimentType(self, readid : str = None) -> str:
return self.getAllHeaders()['experiment_type']
def getFileType(self) -> str:
'''
Returns
-------
file_type : str
'''
return self.getAllHeaders()['file_type']
def getFileVersion(self) -> str:
return self.getAllHeaders()['file_version']
def getFlowCellID(self, readid : str = None) -> str:
return self.getAllHeaders()['flow_cell_id']
def getFlowCellProductCode(self, readid : str = None) -> str:
return self.getAllHeaders()['flow_cell_product_code']
def getGuppyVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['guppy_version']
def getHeatSinkTemp(self, readid : str = None) -> float:
return float(self.getAllHeaders()['heatsink_temp'])
def getHostProductCode(self, readid : str = None) -> str:
return self.getAllHeaders()['host_product_code']
def getHostProductSerialNumber(self, readid : str = None) -> str:
return '' if self.getAllHeaders()['host_product_serial_number'] is None else self.getAllHeaders()['host_product_serial_number']
def getHostname(self, readid : str = None) -> str:
return self.getAllHeaders()['hostname']
def getInstallationType(self, readid : str = None) -> str:
return self.getAllHeaders()['installation_type']
def isLocalBasecalled(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['local_basecalling']))
def getLocalFirmwareFile(self, readid : str = None) -> int:
return int(self.getAllHeaders()['local_firmware_file'])
def getOperatingSystem(self, readid : str = None) -> str:
return self.getAllHeaders()['operating_system']
def getPackage(self, readid : str = None) -> str:
return self.getAllHeaders()['package']
def getPackageVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['package_version']
def getPoreType(self, readid : str = None) -> str:
return self.getAllHeaders()['pore_type']
def getProtocolGroupID(self, readid : str = None) -> str:
return self.getAllHeaders()['protocol_group_id']
def getProtocolRunID(self, readid : str = None) -> str:
return self.getAllHeaders()['protocol_run_id']
def getProtocolStartTime(self, readid : str = None) -> str:
return self.getAllHeaders()['protocol_start_time']
def getProtocolVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['protocols_version']
def getRunID(self, readid : str = None) -> str:
return self.getAllHeaders()['run_id']
def getSampleID(self, readid : str = None) -> str:
return self.getAllHeaders()['sample_id']
def getSequencingKit(self, readid : str = None) -> str:
return self.getAllHeaders()['sequencing_kit']
def getUSBConfig(self, readid : str = None) -> str:
return self.getAllHeaders()['usb_config']
def getVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['version']</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-classes">Classes</h2>
<dl>
<dt id="read5.Slow5Reader.Slow5Reader"><code class="flex name class">
<span>class <span class="ident">Slow5Reader</span></span>
<span>(</span><span>threads: int = 1, batchsize: int = 1, *args, **kwargs)</span>
</code></dt>
<dd>
<div class="desc"><p>File reader for slow5 or blow5 files</p>
<h2 id="attributes">Attributes</h2>
<dl>
<dt><strong><code>threads</code></strong> : <code>int</code></dt>
<dd>number of threads to use in C backend</dd>
<dt><strong><code>batchsize</code></strong> : <code>int</code></dt>
<dd>number of reads to fetch at a time. Higher numbers use more ram, but is more efficient with more threads.</dd>
<dt><strong><code>filepath</code></strong> : <code>str</code></dt>
<dd>Path to the ONT raw data file</dd>
</dl>
<h2 id="raises">Raises</h2>
<dl>
<dt><code>FileNotFoundError</code></dt>
<dd>If the given file does not exist.</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">class Slow5Reader(AbstractFileReader):
'''
File reader for slow5 or blow5 files
Attributes
----------
threads : int
number of threads to use in C backend
batchsize : int
number of reads to fetch at a time. Higher numbers use more ram, but is more efficient with more threads.
filepath : str
Path to the ONT raw data file
Raises
------
FileNotFoundError
If the given file does not exist.
'''
def __init__(self, threads : int = 1, batchsize : int = 1, *args, **kwargs):
self._threads = threads
self._batchsize = batchsize
super().__init__(*args, **kwargs)
def open(self) -> None:
self._file = pyslow5.Open(self._filepath, 'r')
if self._threads > 1:
self._reads = self._file.seq_reads_multi(threads=self._threads, batchsize=self._batchsize)
else:
self._reads, self._nreads = self._file.get_read_ids()
self._open = True
def __getitem__(self, readid : str):
return self._file.get_read(readid)
def getSignal(self, readid : str) -> np.ndarray:
return self.__getitem__(readid)['signal']
def getOffset(self, readid : str) -> float:
return self.__getitem__(readid)['offset']
def getRange(self, readid : str) -> float:
return self.__getitem__(readid)['range']
def getDigitisation(self, readid : str) -> int:
return self.__getitem__(readid)['digitisation']
def getCalibrationScale(self, readid : str) -> float:
return self.getRange(readid) / self.getDigitisation(readid)
def getpASignal(self, readid :str) -> np.ndarray:
return self._file.get_read(readid, pA=True)['signal']
def getChannelNumber(self, readid : str) -> int:
return int(self._file.get_read(readid, aux='channel_number')['channel_number'])
def getStartTime(self, readid : str) -> int:
return self._file.get_read(readid, aux='start_time')['start_time']
def getReadNumber(self, readid : str) -> int:
return self._file.get_read(readid, aux='read_number')['read_number']
def getMedianBefore(self, readid : str) -> int:
return self._file.get_read(readid, aux='median_before')['median_before']
def getStartMux(self, readid : str) -> int:
'''
Returns
-------
start_mux : int
'''
return self._file.get_read(readid, aux='start_mux')['start_mux']
def getEndReason(self, readid : str) -> int:
return self._file.get_read(readid, aux='end_reason')['end_reason']
def getDuration(self, readid : str) -> int:
return self.__getitem__(readid)['len_raw_signal']
def getSamplingRate(self, readid : str) -> int:
return self.__getitem__(readid)['sampling_rate']
### get_all_headers
def getAllHeaders(self) -> dict:
'''
Returns
-------
metadata : dict
all metadata of the sequencing run stored in file.get_all_headers()
'''
return self._file.get_all_headers()
def getAsicID(self, readid : str = None) -> str:
return self.getAllHeaders()['asic_id']
def getAsicIDEeprom(self, readid : str = None) -> str:
return self.getAllHeaders()['asic_id_eeprom']
def getAsicTemp(self, readid : str = None) -> float:
return float(self.getAllHeaders()['asic_temp'])
def getAsicVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['asic_version']
def isAutoUpdated(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['auto_update']))
def getAutoUpdateSource(self, readid : str = None) -> str:
return self.getAllHeaders()['auto_update_source']
def isBarcodingEnabled(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['barcoding_enabled']))
def isBreamStandard(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['bream_is_standard']))
def getConfigurationVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['configuration_version']
def getDeviceID(self, readid : str = None) -> str:
return self.getAllHeaders()['device_id']
def getDeviceType(self, readid : str = None) -> str:
return self.getAllHeaders()['device_type']
def getDistributionStatus(self, readid : str = None) -> str:
return self.getAllHeaders()['distribution_status']
def getDistributionVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['distribution_version']
def getExpScriptName(self, readid : str = None) -> str:
return self.getAllHeaders()['exp_script_name']
def getExpScriptPurpose(self, readid : str = None) -> str:
return self.getAllHeaders()['exp_script_purpose']
def getExpStartTime(self, readid : str = None) -> str:
return self.getAllHeaders()['exp_start_time']
def getExperimentDurationSet(self, readid : str = None) -> int:
return int(self.getAllHeaders()['experiment_duration_set'])
def getExperimentType(self, readid : str = None) -> str:
return self.getAllHeaders()['experiment_type']
def getFileType(self) -> str:
'''
Returns
-------
file_type : str
'''
return self.getAllHeaders()['file_type']
def getFileVersion(self) -> str:
return self.getAllHeaders()['file_version']
def getFlowCellID(self, readid : str = None) -> str:
return self.getAllHeaders()['flow_cell_id']
def getFlowCellProductCode(self, readid : str = None) -> str:
return self.getAllHeaders()['flow_cell_product_code']
def getGuppyVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['guppy_version']
def getHeatSinkTemp(self, readid : str = None) -> float:
return float(self.getAllHeaders()['heatsink_temp'])
def getHostProductCode(self, readid : str = None) -> str:
return self.getAllHeaders()['host_product_code']
def getHostProductSerialNumber(self, readid : str = None) -> str:
return '' if self.getAllHeaders()['host_product_serial_number'] is None else self.getAllHeaders()['host_product_serial_number']
def getHostname(self, readid : str = None) -> str:
return self.getAllHeaders()['hostname']
def getInstallationType(self, readid : str = None) -> str:
return self.getAllHeaders()['installation_type']
def isLocalBasecalled(self, readid : str = None) -> bool:
return bool(int(self.getAllHeaders()['local_basecalling']))
def getLocalFirmwareFile(self, readid : str = None) -> int:
return int(self.getAllHeaders()['local_firmware_file'])
def getOperatingSystem(self, readid : str = None) -> str:
return self.getAllHeaders()['operating_system']
def getPackage(self, readid : str = None) -> str:
return self.getAllHeaders()['package']
def getPackageVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['package_version']
def getPoreType(self, readid : str = None) -> str:
return self.getAllHeaders()['pore_type']
def getProtocolGroupID(self, readid : str = None) -> str:
return self.getAllHeaders()['protocol_group_id']
def getProtocolRunID(self, readid : str = None) -> str:
return self.getAllHeaders()['protocol_run_id']
def getProtocolStartTime(self, readid : str = None) -> str:
return self.getAllHeaders()['protocol_start_time']
def getProtocolVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['protocols_version']
def getRunID(self, readid : str = None) -> str:
return self.getAllHeaders()['run_id']
def getSampleID(self, readid : str = None) -> str:
return self.getAllHeaders()['sample_id']
def getSequencingKit(self, readid : str = None) -> str:
return self.getAllHeaders()['sequencing_kit']
def getUSBConfig(self, readid : str = None) -> str:
return self.getAllHeaders()['usb_config']
def getVersion(self, readid : str = None) -> str:
return self.getAllHeaders()['version']</code></pre>
</details>
<h3>Ancestors</h3>
<ul class="hlist">
<li><a title="read5.AbstractFileReader.AbstractFileReader" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader">AbstractFileReader</a></li>
</ul>
<h3>Methods</h3>
<dl>
<dt id="read5.Slow5Reader.Slow5Reader.getAllHeaders"><code class="name flex">
<span>def <span class="ident">getAllHeaders</span></span>(<span>self) ‑> dict</span>
</code></dt>
<dd>
<div class="desc"><h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>metadata</code></strong> : <code>dict</code></dt>
<dd>all metadata of the sequencing run stored in file.get_all_headers()</dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getAllHeaders(self) -> dict:
'''
Returns
-------
metadata : dict
all metadata of the sequencing run stored in file.get_all_headers()
'''
return self._file.get_all_headers()</code></pre>
</details>
</dd>
<dt id="read5.Slow5Reader.Slow5Reader.getFileType"><code class="name flex">
<span>def <span class="ident">getFileType</span></span>(<span>self) ‑> str</span>
</code></dt>
<dd>
<div class="desc"><h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>file_type</code></strong> : <code>str</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getFileType(self) -> str:
'''
Returns
-------
file_type : str
'''
return self.getAllHeaders()['file_type']</code></pre>
</details>
</dd>
<dt id="read5.Slow5Reader.Slow5Reader.getStartMux"><code class="name flex">
<span>def <span class="ident">getStartMux</span></span>(<span>self, readid: str) ‑> int</span>
</code></dt>
<dd>
<div class="desc"><h2 id="returns">Returns</h2>
<dl>
<dt><strong><code>start_mux</code></strong> : <code>int</code></dt>
<dd> </dd>
</dl></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def getStartMux(self, readid : str) -> int:
'''
Returns
-------
start_mux : int
'''
return self._file.get_read(readid, aux='start_mux')['start_mux']</code></pre>
</details>
</dd>
</dl>
<h3>Inherited members</h3>
<ul class="hlist">
<li><code><b><a title="read5.AbstractFileReader.AbstractFileReader" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader">AbstractFileReader</a></b></code>:
<ul class="hlist">
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.close" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.close">close</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getAsicID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getAsicID">getAsicID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getAsicIDEeprom" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getAsicIDEeprom">getAsicIDEeprom</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getAsicTemp" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getAsicTemp">getAsicTemp</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getAsicVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getAsicVersion">getAsicVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getAutoUpdateSource" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getAutoUpdateSource">getAutoUpdateSource</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getCalibrationScale" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getCalibrationScale">getCalibrationScale</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getChannelNumber" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getChannelNumber">getChannelNumber</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getConfigurationVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getConfigurationVersion">getConfigurationVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getDeviceID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getDeviceID">getDeviceID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getDeviceType" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getDeviceType">getDeviceType</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getDigitisation" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getDigitisation">getDigitisation</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getDistributionStatus" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getDistributionStatus">getDistributionStatus</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getDistributionVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getDistributionVersion">getDistributionVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getDuration" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getDuration">getDuration</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getEndReason" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getEndReason">getEndReason</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getExpScriptName" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getExpScriptName">getExpScriptName</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getExpScriptPurpose" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getExpScriptPurpose">getExpScriptPurpose</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getExpStartTime" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getExpStartTime">getExpStartTime</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getExperimentDurationSet" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getExperimentDurationSet">getExperimentDurationSet</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getExperimentType" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getExperimentType">getExperimentType</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getFilePath" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getFilePath">getFilePath</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getFileVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getFileVersion">getFileVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getFlowCellID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getFlowCellID">getFlowCellID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getFlowCellProductCode" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getFlowCellProductCode">getFlowCellProductCode</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getGuppyVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getGuppyVersion">getGuppyVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getHeatSinkTemp" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getHeatSinkTemp">getHeatSinkTemp</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getHostProductCode" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getHostProductCode">getHostProductCode</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getHostProductSerialNumber" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getHostProductSerialNumber">getHostProductSerialNumber</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getHostname" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getHostname">getHostname</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getInstallationType" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getInstallationType">getInstallationType</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getLocalFirmwareFile" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getLocalFirmwareFile">getLocalFirmwareFile</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getMedianBefore" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getMedianBefore">getMedianBefore</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getOffset" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getOffset">getOffset</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getOperatingSystem" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getOperatingSystem">getOperatingSystem</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getPackage" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getPackage">getPackage</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getPackageVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getPackageVersion">getPackageVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getPolyAStandardizedSignal" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getPolyAStandardizedSignal">getPolyAStandardizedSignal</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getPoreType" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getPoreType">getPoreType</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getProtocolGroupID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getProtocolGroupID">getProtocolGroupID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getProtocolRunID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getProtocolRunID">getProtocolRunID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getProtocolStartTime" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getProtocolStartTime">getProtocolStartTime</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getProtocolVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getProtocolVersion">getProtocolVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getRange" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getRange">getRange</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getReadNumber" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getReadNumber">getReadNumber</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getReads" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getReads">getReads</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getRunID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getRunID">getRunID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getSampleID" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getSampleID">getSampleID</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getSamplingRate" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getSamplingRate">getSamplingRate</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getScale" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getScale">getScale</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getSequencingKit" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getSequencingKit">getSequencingKit</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getShift" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getShift">getShift</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getSignal" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getSignal">getSignal</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getStartTime" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getStartTime">getStartTime</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getStartTimeInMinutes" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getStartTimeInMinutes">getStartTimeInMinutes</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getUSBConfig" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getUSBConfig">getUSBConfig</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getVersion" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getVersion">getVersion</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getZNormSignal" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getZNormSignal">getZNormSignal</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.getpASignal" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.getpASignal">getpASignal</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.isAutoUpdated" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.isAutoUpdated">isAutoUpdated</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.isBarcodingEnabled" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.isBarcodingEnabled">isBarcodingEnabled</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.isBreamStandard" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.isBreamStandard">isBreamStandard</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.isLocalBasecalled" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.isLocalBasecalled">isLocalBasecalled</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.isOpen" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.isOpen">isOpen</a></code></li>
<li><code><a title="read5.AbstractFileReader.AbstractFileReader.open" href="AbstractFileReader.html#read5.AbstractFileReader.AbstractFileReader.open">open</a></code></li>
</ul>
</li>
</ul>
</dd>
</dl>
</section>
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<h4><code><a title="read5.Slow5Reader.Slow5Reader" href="#read5.Slow5Reader.Slow5Reader">Slow5Reader</a></code></h4>
<ul class="">
<li><code><a title="read5.Slow5Reader.Slow5Reader.getAllHeaders" href="#read5.Slow5Reader.Slow5Reader.getAllHeaders">getAllHeaders</a></code></li>
<li><code><a title="read5.Slow5Reader.Slow5Reader.getFileType" href="#read5.Slow5Reader.Slow5Reader.getFileType">getFileType</a></code></li>
<li><code><a title="read5.Slow5Reader.Slow5Reader.getStartMux" href="#read5.Slow5Reader.Slow5Reader.getStartMux">getStartMux</a></code></li>
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