History¶
v0.11.2 (2018-04-16)¶
- Removing
pip
module fromsetup.py
which is not recommended anyway.
v0.11.1 (2018-03-06)¶
- Working around problem in HTSJDK output with incomplete
FORMAT
fields (#127). Writing out.
instead of keeping trailing empty records empty.
v0.11.0 (2017-11-22)¶
- The field
FORMAT/FT
is now expected to be a semicolon-separated string. Internally, we will handle it as a list. - Switching from warning helper utility code to Python
warnings
module. - Return
str
in case of problems with parsing value.
v0.10.0 (2017-02-27)¶
- Extending API to allow for reading subsets of records.
(Writing for sample subsets or reordered samples is possible through using the appropriate
names
list in theSamplesInfos
for theWriter
). - Deep-copying header lines and samples infos on
Writer
construction - Using
samples
attribute fromHeader
inReader
andWriter
instead of passing explicitely
0.9.0 (2017-02-26)¶
- Restructuring of requirements.txt files
- Fixing parsing of no-call
GT
fields
0.8.1 (2017-02-08)¶
- PEP8 style adjustments
- Using versioneer for versioning
- Using
requirements*.txt
files now from setup.py - Fixing dependency on cyordereddict to be for Python <3.6 instead of <3.5
- Jumping by samtools coordinate string now also allowed
0.8.0 (2016-10-31)¶
- Adding
Header.has_header_line
for querying existence of header line Header.add_*_line
return abool
no indicating any conflicts- Construction of Writer uses samples within header and no extra parameter (breaks API)
0.7.0 (2016-09-25)¶
- Smaller improvements and fixes to documentation
- Adding Codacy coverage and static code analysis results to README
- Various smaller code cleanup triggered by Codacy results
- Adding
__eq__
,__neq__
and__hash__
to data types (where applicable)
0.6.0 (2016-09-25¶
- Refining implementation for breakend and symbolic allele class
- Removing
record.SV_CODES
- Refactoring parser module a bit to make the code cleaner
- Fixing small typos and problems in documentation
0.5.0 (2016-09-24)¶
- Deactivating warnings on record parsing by default because of performance
- Adding validation for
INFO
andFORMAT
fields on reading (#8) - Adding predefined
INFO
andFORMAT
fields topyvcf.header
(#32)
0.4.1 (2016-09-22)¶
- Initially enabling codeclimate
0.4.0 (2016-09-22)¶
- Exporting constants for encoding variant types
- Exporting genotype constants
HOM_REF
,HOM_ALT
,HET
- Implementing
Call.is_phased
,Call.is_het
,Call.is_variant
,Call.is_phased
,Call.is_hom_ref
,Call.is_hom_alt
- Removing
Call.phased
(breaks API, next release is 0.4.0) - Adding tests, fixing bugs for methods of
Call
0.3.1 (2016-09-21)¶
- Work around
FORMAT/FT
being a string; this is done so in the Delly output
0.3.0 (2016-09-21)¶
Reader
andWriter
can now be used as context manager (withwith
)- Including license in documentation, including Biopython license
- Adding support for writing bgzf files (taken from Biopython)
- Adding support for parsing arrays in header lines
- Removing
example-4.1-bnd.vcf
example file because v4.1 tumor derival lacksID
field - Adding
AltAlleleHeaderLine
,MetaHeaderLine
,PedigreeHeaderLine
, andSampleHeaderLine
- Renaming
SimpleHeaderFile
toSimpleHeaderLine
- Warn on missing
FILTER
entries on parsing - Reordered parameters in
from_stream
andfrom_file
(#18) - Renamed
from_file
tofrom_stream
(#18) - Renamed
Reader.jump_to
toReader.fetch
- Adding
header_without_lines
function - Generally extending API to make it esier to use
- Upgrading dependencies, enabling pyup-bot
- Greatly extending documentation
0.2.1 (2016-09-19)¶
- First release on PyPI