CHANGELOG.md

v1.2.23

• Build using python3.5
• Fix bug with shuffle option within fast5.py
• Allow None as an input to BulkFast5.get_raw
• Allow summary file to use strand_duration instead of strand as column name

v1.2.22

• Update way reads classifications are parsed from the bulk to use modal classification as Minknow now does.

v1.2.21

• Add filter_from_bam command to create filter tsv file from BAM and sequencing summary file.

v1.2.20

• Add index_reads program to build read_id->file index tsv file.

v1.2.19

• Add program to produce read summary text file from Bulk .fast5.

v1.2.18

• Allow extract_reads to extract only reads present in a given read_summary.txt

v1.2.17

• Allow filter_reads to be given full filename/read_id information

v1.2.16

• Fix bug in filter_reads resulting in the last worker's reads not being written.

v1.2.15

• Calculate drift from read table as it will no longer be present in the read table.

v1.2.14

• Fix issue affecting conversion of |u1 dtypes

v1.2.13

• Use filename if possible when extracting reads

v1.2.12

• Clear up a deprecation warning: https://github.com/nanoporetech/fast5_research/issues/30

v1.2.11

• Add filter_reads program to extract a subset of reads from multi-reads.

v1.2.10

• Minor syntax fix in extract.py for python2

v1.2.9

• Add basic support for creation of multi-read files from bulk files.

v1.2.8

• Small refactor of writing of mapping data.

v1.2.6

• Fix slow creation of mapping table

v1.2.5

• Ensure event structures containing text data are returned as strings rather than bytes under python3.

v1.2.3

• Fixes issue with numpy 1.15 on reading type of views of structured data.
• Updated documentation (https://nanoporetech.github.io/fast5_research/)

v1.2.2

• Conversion from bulk to reads.
• Require numpy >= 1.14.
• A bit more python3 bytes cleaning.
• Enforce types in raw, and required tracking_id attributes.

v1.1.0

• Python3 compatibility changes
• Add data cleaning steps for stringly types
• Unpin numpy version

v1.0.12

• Enforce some typing constraints on meta data for compatibility with some basecallers.

v1.0.11

• Ignore h5py warnings on import

v1.0.10

• Fix bug finding attributes when EventDetection not present

v1.0.8

• Easy import of core classes and functions: from fast5_research import Fast5, BulkFast5, iterate_fast5
• Enable recursive (lazy) search in iterate_fast5.

v1.0.9

• Fix itertools import

v1.0.6

• Ensure returned events have same dtype
• fast5.py: all returned event arrays same dtype by passing them through self._get_read_data()
• requirements: use any version of numpy
• bump version to 1.0.6