Bugfix release to solve compilation issue due to missinge bcftools/config.h file.
This release wraps htslib/samtools/bcftools versions 1.5.0 and contains a series of bugfixes.
[#473] A new FastxRecord class that can be instantiated from class and modified in-place. Replaces PersistentFastqProxy.
[#521] In AligmentFile, Simplify file detection logic and allow remote index files * Removed attempts to guess data and index file names; this is magic left
- Removed file existence check prior to opening files with htslib
- Better error checking after opening files that raise the appropriate error (IOError for when errno is set, ValueError otherwise for backward compatibility).
- Report IO errors when loading an index by name.
- Allow remote indices (tested using S3 signed URLs).
- Document filepath_index and make it an alias for index_filename.
- Added a require_index parameter to AlignmentFile
[#526] handle unset ref when creating new records
[#513] fix bcf_translate to skip deleted FORMAT fields to avoid segfaults
[#516] expose IO errors via IOError exceptions
[#487] add tabix line_skip, remove ‘pileup’ preset
add FastxRecord, replaces PersistentFastqProxy (still present for backwards compatibility)
[#496] upgrade to htslib/samtools/bcftools versions 1.5
add start/stop to AlignmentFile.fetch() to be consistent with VariantFile.fetch(). “end” is kept for backwards compatibility.
[#512] add get_index_statistics() method to AlignmentFile.
In the next release we are plannig to separate the header information from AlignmentFile into a separate class AlignmentHeader. This layout is similar to VariantFile/VariantHeader. With this change we will ensure that an AlignedSegment record will be linked to a header so that chromosome names can be automatically translated from the numeric representation. As a consequence, the way new AlignedSegment records are created will need to change as the constructor requires a header:
header = pysam.AlignmentHeader( reference_names=["chr1", "chr2"], reference_lengths=[1000, 1000]) read = pysam.AlignedSegment(header)
This will affect all code that instantiates AlignedSegment objects directly. We have not yet merged to allow users to provide feed-back. The pull-request is here: https://github.com/pysam-developers/pysam/pull/518 Please comment on github.
Bugfix release to address two issues:
- Changes in 0.11.2.1 broke the GTF/GFF3 parser. Corrected and more tests have been added.
- [#479] Correct VariantRecord edge cases described in issue
Release to fix release tar-ball containing 0.11.1 pre-compiled C-files.
This release wraps htslib/samtools/bcfools versions 1.4.1 in response to a security fix in these libraries. Additionaly the following issues have been fixed:
- [#452] add GFF3 support for tabix parsers
- [#461] Multiple fixes related to VariantRecordInfo and handling of INFO/END
- [#447] limit query name to 251 characters (only partially addresses issue)
VariantFile and related object fixes
- Restore VariantFile.__dealloc__
- Correct handling of bcf_str_missing in bcf_array_to_object and bcf_object_to_array
- Added update() and pop() methods to some dict-like proxy objects
- scalar INFO entries could not be set again after being deleted
- VariantRecordInfo.__delitem__ now allows unset flags to be deleted without raising a KeyError
- Multiple other fixes for VariantRecordInfo methods
- INFO/END is now accessible only via VariantRecord.stop and VariantRecord.rlen. Even if present behind the scenes, it is no longer accessible via VariantRecordInfo.
- Add argument to issue a warning instead of an exception if input appears to be truncated
Other features and fixes:
- Make AlignmentFile __dealloc__ and close more stringent
- Add argument AlignmentFile to issue a warning instead of an exception if input appears to be truncated
- [#440] add deprecated ‘always’ option to infer_query_length for backwards compatibility.
This release wraps the latest versions of htslib/samtools/bcftools and implements a few bugfixes.
- [#413] Wrap HTSlib/Samtools/BCFtools 1.4
- [#422] Fix missing pysam.sort.usage() message
- [#411] Fix BGZfile initialization bug
- [#412] Add seek support for BGZFile
- [#395] Make BGZfile iterable
- [#433] Correct getQueryEnd
- [#419] Export SAM enums such as pysam.CMATCH
- [#415] Fix access by tid in AlignmentFile.fetch()
- [#405] Writing SAM now outputs a header by default.
- [#332] split infer_query_length(always) into infer_query_length and infer_read_length
This release implements further functionality in the VariantFile API and includes several bugfixes:
- treat special case -c option in samtools view outputs to stdout even if -o given, fixes #315
- permit reading BAM files with CSI index, closes #370
- raise Error if query name exceeds maximum length, fixes #373
- new method to compute hash value for AlignedSegment
- AlignmentFile, VariantFile and TabixFile all inherit from HTSFile
- Avoid segfault by detecting out of range reference_id and next_reference in AlignedSegment.tostring
- Issue #355: Implement streams using file descriptors for VariantFile
- upgrade to htslib 1.3.2
- fix compilation with musl libc
- Issue #316, #360: Rename all Cython modules to have lib as a prefix
- Issue #332, hardclipped bases in cigar included by pysam.AlignedSegment.infer_query_length()
- Added support for Python 3.6 filename encoding protocol
- Issue #371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord
- Issue #331, fix failure in VariantFile.reset() method
- Issue #314, add VariantHeader.new_record(), VariantFile.new_record() and VariantRecord.copy() methods to create new VariantRecord objects
- Added VariantRecordFilter.add() method to allow setting new VariantRecord filters
- Preliminary (potentially unsafe) support for removing and altering header metadata
- Many minor fixes and improvements to VariantFile and related objects
Please note that all internal cython extensions now have a lib prefix to facilitate linking against pysam extension modules. Any user cython extensions using cimport to import pysam definitions will need changes, for example:
This is a bugfix release addressing some installation problems in pysam 0.9.0, in particular:
- patch included htslib to work with older libcurl versions, fixes #262.
- do not require cython for python 3 install, fixes #260
- FastaFile does not accept filepath_index any more, see #270
- add AlignedSegment.get_cigar_stats method.
- py3 bugfix in VariantFile.subset_samples, fixes #272
- add missing sysconfig import, fixes #278
- do not redirect stdout, but instead write to a separately created file. This should resolve issues when pysam is used in notebooks or other environments that redirect stdout.
- wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1
- use bgzf throughout instead of gzip
- allow specifying a fasta reference for CRAM file when opening for both read and write, fixes #280
The 0.9.0 release upgrades htslib to htslib 1.3 and numerous other enchancements and bugfixes. See below for a detailed list.
comes with additional capabilities for remote file access which depend
on the presence of optional system libraries. As a consequence, the
setup.py has become more complex. For an
overview, see Installing pysam. We have tested installation on
linux and OS X, but could not capture all variations. It is possible
that a 0.9.1 release might follow soon addressing installation issues.
Detailed release notes¶
upgrade to htslib 1.3
python 3 compatibility tested throughout.
added a first set of bcftools commands in the pysam.bcftools submodule.
samtools commands are now in the pysam.samtools module. For backwards compatibility they are still imported into the pysam namespace.
samtools/bcftools return stdout as a single (byte) string. As output can be binary (VCF.gz, BAM) this is necessary to ensure py2/py3 compatibility. To replicate the previous behaviour in py2.7, use:
get_tags() returns the tag type as a character, not an integer (#214)
TabixFile now raises ValueError on indices created by tabix <1.0 (#206)
improve OSX installation and develop mode
FastxIterator now handles empty sequences (#204)
TabixFile.isremote is not TabixFile.is_remote in line with AlignmentFile
AlignmentFile.count() has extra optional argument read_callback
- setup.py has been changed to:
- install a single builtin htslib library. Previously, each pysam module contained its own version. This reduces compilation time and code bloat.
- run configure for the builtin htslib library in order to detect optional libraries such as libcurl. Configure behaviour can be controlled by setting the environmet variable HTSLIB_CONFIGURE_OPTIONS.
get_reference_sequence() now returns the reference sequence and not something looking like it. This bug had effects on get_aligned_pairs(with_seq=True), see #225. If you have relied on on get_aligned_pairs(with_seq=True) in pysam-0.8.4, please check your results.
improved autodetection of file formats in AlignmentFile and VariantFile.
This release contains numerous bugfixes and a first implementation of a pythonic interface to VCF/BCF files. Note that this code is still incomplete and preliminary, but does offer a nearly complete immutable Pythonic interface to VCF/BCF metadata and data with reading and writing capability.
Potential isses when upgrading from v0.8.3:
binary tags are now returned as python arrays
renamed several methods for pep8 compatibility, old names still retained for backwards compatibility, but should be considered deprecated.
- gettid() is now get_tid()
- getrname() is now get_reference_name()
- parseRegion() is now parse_region()
some methods have changed for pep8 compatibility without the old names being present:
- fromQualityString() is now qualitystring_to_array()
- toQualityString() is now qualities_to_qualitystring()
faidx now returns strings and not binary strings in py3.
The cython components have been broken up into smaller files with more specific content. This will affect users using the cython interfaces.
Edited list of commit log changes:
- fixes AlignmentFile.check_index to return True
- add RG/PM header tag - closes #179
- add with_seq option to get_aligned_pairs
- use char * inside reconsituteReferenceSequence
- add soft clipping for get_reference_sequence
- add get_reference_sequence
- queryEnd now computes length from cigar string if no sequence present, closes #176
- tolerate missing space at end of gtf files, closes #162
- do not raise Error when receiving output on stderr
- add docu about fetching without index, closes #170
- FastaFile and FastxFile now return strings in python3, closes #173
- py3 compat: relative -> absolute imports.
- add reference_name and next_reference_name attributes to AlignedSegment
- add function signatures to cvcf cython. Added note about other VCF code.
- add context manager functions to FastaFile
- add reference_name and next_reference_name attributes to AlignedSegment
- PileupColumn also gets a reference_name attribute.
- add context manager functions to FastaFile
- TabixFile.header for remote files raises AttributeError, fixes #157
- add context manager interface to TabixFile, closes #165
- change ctypedef enum to typedef enum for cython 0.23
- add function signatures to cvcf cython, also added note about other VCF code
- remove exception for custom upper-case header record tags.
- rename VALID_HEADER_FIELDS to KNOWN_HEADER_FIELDS
- fix header record tag parsing for custom tags.
- use cython.str in count_coverage, fixes #141
- avoid maketrans (issues with python3)
- refactoring: AlignedSegment now in separate module
- do not execute remote tests if URL not available
- fix the unmapped count, incl reads with no SQ group
- add raw output to tags
- added write access for binary tags
- bugfix in call to resize
- implemented writing of binary tags from arrays
- implemented convert_binary_tag to use arrays
- add special cases for reads that are unmapped or whose mates are unmapped.
- rename TabProxies to ctabixproxies
- remove underscores from utility functions
- move utility methods into cutils
- remove callback argument to fetch - closes #128
- avoid calling close in dealloc
- add unit tests for File object opening
- change AlignmentFile.open to filepath_or_object
- implement copy.copy, close #65
- add chaching of array attributes in AlignedSegment, closes #121
- add export of Fastafile
- remove superfluous pysam_dispatch
- use persist option in FastqFile
- get_tag: expose tag type if requested with with_value_type
- fix to allow reading vcf record info via tabix-based vcf reader
- add pFastqProxy and pFastqFile objects to make it possible to work with multiple fastq records per file handle, unlike FastqProxy/FastqFile.
- release GIL around htslib IO operations
- More work on read/write support, API improvements
- add phased property on VariantRecordSample
- add mutable properties to VariantRecord
- BCF fixes and start of read/write support
- VariantHeaderRecord objects now act like mappings for attributes.
- add VariantHeader.alts dict from alt ID->Record.
- Bug fix to strong representation of structured header records.
- VariantHeader is now mutable
- samtools command now accept the “catch_stdout” option.
- get_aligned_pairs now works for soft-clipped reads.
- query_position is now None when a PileupRead is not aligned to a particular position.
- AlignedSegments are now comparable and hashable.
- Installation bugfix release.
- Pysam now wraps htslib 1.2.1 and samtools version 1.2.
- Added CRAM file support to pysam.
- New alignment info interface.
- opt() and setTag are deprecated, use get_tag() and set_tag() instead.
- added has_tag()
- tags is deprecated, use get_tags() and set_tags() instead.
- FastqFile is now FastxFile to reflect that the latter permits iteration over both fastq- and fasta-formatted files.
- A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper provides a nearly complete Pythonic interface to VCF/BCF metadata with reading and writing capability. However, the interface is still incomplete and preliminary and lacks capability to mutate the resulting data.
- Pysam now wraps htslib and samtools versions 1.1.
- Bugfixes, most notable: * issue #43: uncompressed BAM output * issue #42: skip tests requiring network if none available * issue #19: multiple iterators can now be made to work on the same tabix file * issue #24: All strings returned from/passed to the pysam API are now unicode in python 3 * issue #5: type guessing for lists of integers fixed
- API changes for consistency. The old API is still present,
- Tabixfile -> TabixFile
- Fastafile -> FastaFile
- Fastqfile -> FastqFile
- Samfile -> AlignmentFile
- AlignedRead -> AlignedSegment
- qname -> query_name
- tid -> reference_id
- pos -> reference_start
- mapq -> mapping_quality
- rnext -> next_reference_id
- pnext -> next_reference_start
- cigar -> cigartuples
- cigarstring -> cigarstring
- tlen -> template_length
- seq -> query_sequence
- qual -> query_qualities, now returns array
- qqual -> query_alignment_qualities, now returns array
- tags -> tags
- alen -> reference_length, reference is always “alignment”, so removed
- aend -> reference_end
- rlen -> query_length
- query -> query_alignment_sequence
- qstart -> query_alignment_start
- qend -> query_alignment_end
- qlen -> query_alignment_length
- mrnm -> next_reference_id
- mpos -> next_reference_start
- rname -> reference_id
- isize -> template_length
- blocks -> get_blocks()
- aligned_pairs -> get_aligned_pairs()
- inferred_length -> infer_query_length()
- positions -> get_reference_positions()
- overlap() -> get_overlap()
- All strings are now passed to or received from the pysam API as strings, no more bytes.
- Other changes:
- AlignmentFile.fetch(reopen) option is now multiple_iterators. The default changed to not reopen a file unless requested by the user.
- FastaFile.getReferenceLength is now FastaFile.get_reference_length
Backwards incompatible changes
- Empty cigarstring now returns None (intstead of ‘’)
- Empty cigar now returns None (instead of )
- When using the extension classes in cython modules, AlignedRead needs to be substituted with AlignedSegment.
- fancy_str() has been removed
- qual, qqual now return arrays
- Disabled features
- IteratorColumn.setMask() disabled as htslib does not implement this functionality?
- Not implemented yet:
- reading SAM files without header
Tabix files between version 0.7.8 and 0.8.0 are not compatible and need to be re-indexed.
While version 0.7.8 and 0.8.0 should be mostly compatible, there are some notable exceptions:
- tabix iterators will fail if there are comments in the middle or the end of a file.
- tabix raises always ValueError for invalid intervals. Previously, different types of errors were raised (KeyError, IndexError, ValueError) depending on the type of invalid intervals (missing chromosome, out-of-range, malformatted interval).
- added AlignedRead.setTag method
- added AlignedRead.blocks
- unsetting CIGAR strings is now possible
- empty CIGAR string returns empty list
- added reopen flag to Samfile.fetch()
- various bugfixes
- added Fastafile.references, .nreferences and .lengths
- tabix_iterator now uses kseq.h for python 2.7
- added inferred_length property
- issue 122: MACOSX getline missing, now it works?
- seq and qual can be set None
- added Fastqfile
- switch to samtools 0.1.19
- issue 122: MACOSX getline missing
- issue 130: clean up tempfiles
- various other bugfixes
- further bugfixes to setup.py and package layout
- further bugfixes to setup.py
- upgraded distribute_setup.py to 0.6.34
- bugfix in installer - failed when cython not present
- changed installation locations of shared libraries
- bugfix: missing PP tag PG records in header
- added pre-built .c files to distribution
- switch to tabix 0.2.6
- added cigarstring field
- python3 compatibility
- added B tag handling
- added check_sq and check_header options to Samfile.__init__
- added lazy GTF parsing to tabix
- reworked support for VCF format parsing
- switch to samtools 0.1.18
- various bugfixes
- removed references to deprecated ‘samtools pileup’ functionality
- AlignedRead.tags now returns an empty list if there are no tags.
- added pnext, rnext and tlen
- switch to samtools 0.1.16 and tabix 0.2.5
- improved tabix parsing, added vcf support
- re-organized code to permit linking against pysam
- various bugfixes
- added Samfile.positions and Samfile.overlap
- switch to samtools 0.1.12a and tabix 0.2.3
- added snp and indel calling.
- switch from pyrex to cython
- changed handling of samtools stderr
- various bugfixes
- added Samfile.count and Samfile.mate
- deprecated AlignedRead.rname, added AlignedRead.tid
- switch to samtools 0.1.8
- added support for tabix files
- numerous bugfixes including
- permit simultaneous iterators on the same file
- working access to remote files