readtagger 0.5.9

0.5.9 (2018-08-31)

Fix crash when corrected start/end can’t be calculated.

0.5.8 (2018-08-31)

Improve joining of clusters

0.5.7 (2018-08-29)

Don’t mark clusters incompatible after splitting them out from original cluster Use corrected or uncorrected start/end when finding reachable clusters Also allow joining with downstream reverse cluster Detect local maximum proper pair size

0.5.6 (2018-08-28)

Always produce contig fasta, required for refining cluster positions Allow +/- 10 nucleotides between alignment and insert start/end

0.5.5 (2018-08-27)

• Add timeout to cap3 call

• Update dependencies

0.5.4 (2018-07-29)

• Bump pysam dependency to 0.15.3, contains important fixes

0.5.3 (2018-07-28)

• Sort ‘extract_variants’ output alignment

0.5.2 (2018-07-28)

• Add ‘extract_variants’ tool for extracting insertion evidence from long reads

0.5.1 (2018-06-13)

• Only associate clipping pattern with insertion if pattern matches breakpoint sequence

0.5.0 (2018-06-12)

• Drop support for Python 2

0.4.20 (2018-06-12)

• Keep all associated softclip patterns when merging adjacent read clusters

0.4.19 (2018-02-15)

• Fix findcluster crash when reference contains colon.

0.4.18 (2018-02-14)

• Use logger.warning instead of deprecated logger.warn

• Drop now unused qname_cmp_func

• Fix alignment splitting, fixes untagged reads and speed issues

0.4.17 (2018-02-10)

• Fix a bug that would lead to wrong chunk sizes

0.4.16 (2018-01-28)

• Drop samtools, do everything via pysam

0.4.15 (2018-01-15)

• Add missing samtools dependency

0.4.14 (2018-01-15)

• Build Conda package for python 3 only

0.4.13 (2018-01-14)

• Update pinned dependencies

• Fix travis deployment

0.4.12 (2018-08-21)

• Allow multiple inputs to readtagger

• Allow passing multiple control files to confirm_insertions script

• Fix matching of short 3p clipped sequences

0.4.11 (2018-05-18)

• Add a script that merges findlcuster VCF output

• Allow 5 nt overlaps at cluster consistency check

• Include VALID_TSD in INFO field and write out PE support

• Sort output VCF file

• Generate IDs using reference_name start and cluster order

• Improve support for arbitrary insertion names

0.4.10 (2018-03-30)

• Include unmapped but tagged mates in veriefied tags

• Update findcluster galaxy tool and fix softclip cluster ids

• Use a unique ID as variant ID

• Stop collection evidence once we reach 10000 reads

• Speed up finding of soft clip clusters

• Implement VCF output

• Make loglevel configurable for findcluster script and add option to output log to file

• Look for softclipped reads in a 15nt window and compare 5p clips by their end

• Add script and tool to confirm/reject insertions

• Refine the detection of TE clusters that are very close to each other

• Verify that reads really support a specific insertion

• Fix sorting to CRAM output

• Move sorting of softclip clusters to merging phase

• Skip finding softclipped clusters when skipping TE clusters

• Annotate softclips as part of TEs

• Embedd SoftClipClusterFinder in ClusterFinder

• Fix softclipped positions when read contains deletions

0.4.9 (2018-01-23)

• Fix deployment to PyPI

0.4.8 (2018-01-23)

• Update test data output and allow :

• Add edlib to requirements in setup.py

• Add softclip finder test

• Build on python-3.6

• Make futures library conditional for python2

• Drop temporary from requirements

• Extend testcoverage

• Drop external_bin from BamAlignmentWriter

• Many small simplifications, bugfixes and enhaced tests

• Improve reporting of 5p and 3p clips

• Add some wigglespace for finding the most likely TSD position

• Keep insertions associated with deletion intact

• Add testcase for a cluster that should not be split

• Fix if/else logic for genotypes

• Skip “genomic sinks” with lots of TE evidence

• Continue on RuntimeError

• Improve splitting of input file

• Need to fetch reads in the specified region if using external_bin=False

• Don’t use external samtools when finding clusters

• Identify decoy regions based on cluster density

• Drop reraise_with_stack, doesn’t work on py3

• Fix outdated min/max coordinates leading to dropped chunks

• Re-raise any exceptions when processing chunks

• Fix OrderedDict syntax for py2 compatibility

• Improve logging when splitting input into chunks

• Don’t remove read that isn’t present anymore

• Fix return value when assembling too many reads

• Fix limiting of region when using multiple threads

• Report maximum MAPQ of read evidence for a cluster

• Bump minimum MAPQ to 4 by default and make it configurable

• Refactor cap3 assembly (so it can be exchanged more easily) and add limit to how many reads it will assemble

• Fix and apply read_is_compatible to all read with BD tag

• Generalize marking clusters as compatible or incompatible and apply at every cluster split or join

• Estimate nref/nalt using overlap of start and end if start and end are more than 50nt apart

• Skip clusters of reads that are inconsistent

• Remove redundant parenthesis, fix typo

• Allow non-proper pairs when counting evidence

• Account for max. mate distance when joining cluster

• Add new dependencies to conda recipe

• Prevent joining clusters that we previously split explicitly

• Don’t thread/cache joining of cluster

• Use lru_cache for some cigar operations

• Use cigar_to_max function consistently

• Make use of new AlignmentHeader object (old method now very slow)

• Use edlib align instead of Cap3Assembly

• Fix evidence_against functionality

• Output reads that count as non-support

• Allow picking up location of reference_fasta via env var for quicker test execution

• Fix 3p evidence bam, fix nref with 1 breakpoint

• Update test-data

• Assign left/right based on AD if AD and BD are set

• Make counting more accurate, cleanup various Cluster counts and write out split reads found via evidence_for_five/three_p

• Collect evidence for insertions

• Fix a typo in get_breakpoint_sequence

• Fix resolving consensus ties if tie contains N

• Upgrade to pysam 0.14

• Make split_ads a property since the splits can update

• Fix typo in dumb_consensus help

• Add IUPAC to nucleotides dict

• Restructure non_evidence so that evidence for and against can be counted

• Use reference_start instead of deprecated pos

• Implement get_breakpoint_sequence as a method of TargetSiteDuplication

• Add evidence_for function

• Update planemo from 0.46.1 to 0.48.0

• Refine the cluster merging logic

• Fix the overlap calculation, in case the re-aligned contig ends up at a different position

• Update test data output, genotype outputs with higher precision (sigh)

0.4.7 (2018-01-23)

• Fix Exception that occurs when cluster doesn’t have an associated contig

• Fix TE alignment logic when using pre-indexed transposon references

• Control which reads extend a cluster during cluster refinement

• Add a safeguard to avoid merging unrelated, far-away clusters

0.4.6 (2017-12-13)

• Deploy to conda on py3 as well

• Make sure cluster chunks are ordered

• Avoid hangs due to expection in multiprocessing tasks

0.4.2 (2017-12-13)

• Fix passing of region specification to pileup engine

• Point out typical useage of –reference_fasta and –reference_index

• Fix cheetah bwa index variable for findcluster galaxy tool

0.4.1 (2017-11-20)

• Add matplotlib and pandas to dependencies

• Add a script that can plot coverage as an area plot between two bam files

• Update dependencies

• If either three_p or five_p of a tsd is unknown assign the available use the available side to test of a read belongs to the left or right side of an insertion

• Fix crash for unaligned(?) reads

• Change deprecacted alen, pos and mpos to current replacements

• Tune clusterfinding for misaligned long reads

0.4.0 (2017-11-09)

• Fixes for CRAM input and output

• Adjust chunk-size in readtagger based on readlength (for pacbio/nanopore reads)

• Cleanup temporary bwa indexes

• Dependency updates

0.3.25 (2017-06-21)

• Refine cluster coordinates using an Assembly strategy

• Fix GFF sorting on python 3

• Improve BWA alignment settings (default to intractg plus -Y) and add align_contigs method to SimpleAligner

• Add pysamtools_view command

• Improve cluster-splitting

• Add multiprocessing-logging recipe

• Only output BWA stderr if the exit code is not zero

• Add a function to sort gff files

• Close open file descriptors

• Make imprecise insertion sites more realistic

• Fix read_index property

• Adapt readtagger to higher coverage datasets

• Fix readtagger crash when not producing discard tag file.

• Add number of mates for left and right support to GFF

• Split clusters that start with reverse reads conatining only BD tags

0.3.24 (2017-05-11)

• Split cluster if there are multiple polarity switches between Forward and Reverse orientation

• Manipulate copy of cigarlist to avoid numpy issue

0.3.23 (2017-05-09)

• Expose reference fasta option in bam_readtagger.xml

0.3.22 (2017-05-09)

• Move readtagger CLI form argparse to click

• Index bamfile if neccesary

• Replace multipocessing pool with ProcessPoolExecutor

• Set the matesequence while tagging reads

• Fix false positives in readtagger module

• Do cap3 assembly in shared memory if passing –shm_dir or if SHM_DIR environment variable is defined

• Parallelize findlcluster by splitting input bam

• Add check_call.py script for rapidly verifying IGV screenshots

0.3.21 (2017-04-27)

• Fix crash when determining reference name

0.3.20 (2017-04-27)

• Guess the best TE match and write it into GFF Parent

• Fix case where input files are already sorted

• Remove blast from requirements

0.3.19 (2017-04-27)

• Skip creating tempdirs in current working directory

• Remove blast-specific files

• Switch to using BWA for annotating detected insertions

• Add more logging and default to not changing sort order unless specifically demanded

• Do dovetailing on coordinate-sorted file

0.3.18 (2017-04-25)

• Fix small outputs due to switching of -t and -a options

0.3.17 (2017-04-25)

• Fix file seeking

• Update dependencies

0.3.16 (2017-04-23)

• Parallelize readtagger

0.3.15 (2017-04-20)

• Do not count reads as support if both AD and BD tag contribute to an insertion

• Remove sambamba support

0.3.14 (2017-04-19)

• Perform readtagging on readname sorted files.

• Catch possible errors

• Add BWA alignment module to replace Blast

0.3.13 (2017-04-05)

• Add possibility to output cluster contigs as fasta

0.3.12 (2017-03-31)

• Fix and accelerate the calculation of nref (=non support evidence)

• Update priors and genotype frequrencies to a more realistic model

0.3.11 (2017-03-28)

• Add a testcase for genotyping module

• Stream over full alignment file instead of fetching regions, pysam.AlignmentFile.fetch is too slow

0.3.10 (2017-03-26)

• Revert local conda dependency resolution

• Fix readtagger.add_mate to work also if one mate is unmapped

0.3.9 (2017-03-26)

• Add a genotyping module

• Keep tags for alternative alignments if mates are not in a proper pair

0.3.4 (2017-03-02)

• Speed up assembly steps using multithreading

• Implement a cache for the Cluster.can_join method

0.3.3 (2017-03-02)

• Fix a crash when writing GFF for a cluster of hardclipped reads

• Change confusing variable names and copypasted docstring

0.3.2 (2017-03-02)

• Fix another crash when tuple starts with 1,2,7 or 8

0.3.1 (2017-03-02)

• Fix a crash when a mismatch is the last item in a cigartuple

0.3.0 (2017-03-02)

• Add a galaxy tool for the findcluster script

• Add new script that finds clusters of reads and outputs GFF or BAM files with these clusters.

• Implement writing clusters as GFF files

• Implement writing out reads with cluster number annotated in CD tag.

• Implement merging of clusters based on whether reads contribute to common contigs

• Use cached-property where it makes sense

• Add module to find, join and annotate clusters of reads

• Represent cigartuple as namedtuple

• Add a Roadmap file

• Add more logic for finding ends of insertions and

• Manipulate cluster of reads to find TSDs

• Add module for cap3 assembly and manipulation of assembled reads

• Fix conda recipe script entrypoints

0.2.0 (2017-02-21)

• Reformat help text in galaxy wrappers

• Add add_matesequence script to add the sequence of the mate of the current read as a tag

• Add option to discard alternative tag if read is a proper pair

• Stitch cigars that are separated by I or D events

• Add a tag tuple that knows how to format itself

• Update README.rst example with current default tag prefix

• Test with and without discarding verified reads

• Symlink test-files that are shared with the galaxy test, add testcase for allow_dovetailing script

• Fix HISTORY.rst formatting

0.1.13(2017-02-17)

• Add instructions for development

• Install planemo in deployment step

0.1.12(2017-02-17)

• Test deployment again

0.1.11 (2017-02-17)

• Test deployment

0.1.10 (2017-02-17)

• Fix toolshed deployment

0.1.9 (2017-02-17)

• Add automated deployment to Galaxy Toolshed

• Add instructions for development and release process

0.1.8 (2017-02-17)

• Minor release to test release process

0.1.7 (2017-02-17)

• Extend testing with coverage testing

• Automate deployment to pypi and conda

• Register project with pyup.io

0.1.6 (2017-02-16)

• Rename to readtagger

• Fix bug with stdin closing file descriptor too early, leading to corrupt BAM files

• Extend testing

0.1.5 (2017-02-12)

• Add option (-wd) to write suboptimal tag into separate BAM file

• Add option (-wv) to write verified tags into separate BAM file

• Performance improvments by letting sambamba handle BAM reading and writing. Also elimininate regualr expression to parse cigarstring

0.1.4 (2017-02-10)

• Add option (-k) to keep alternative tags if they do not explain the softclipped read any better. Default is to discard them.

0.1.3.2 (2017-02-08)

• Fix dovetailing script

0.1.3 (2017-02-07)

• Add option to allow dovetailing in alignment files when tagging reads

• Add separate entrypoint for standalone script

0.1.2 (2017-02-05)

• Add conda recipe

• Python3 string fix

0.1.0 (2017-02-05)

• Initial version