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Changelog
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Changelog
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2023-02-14 Youri Hoogstrate v0.18.3
* when provided the appropriate discordant reads (i.e. no cannonical reads) from the master bam,
`dr-disco fix` should be able to correctly fix those.
Detailed bug report by Marcel Smid, thanks
* got rid of fuma dependency
2022-04-20 Youri Hoogstrate v0.18.2
* strict mode for dr-disco bam-extract querying only targeted chromosomes/reference_nams
2020-03-25 Youri Hoogstrate v0.18.1
* blacklist regions and junctions 'chr' prefix insensitive
2019-12-04 Youri Hoogstrate v0.18.0
* Ported to python3
2018-12-05 Youri Hoogstrate v0.17.7
* Updates to blacklist
2018-12-03 Youri Hoogstrate v0.17.6
* Updates to blacklist
2018-09-12 Youri Hoogstrate v0.17.5
* `dr-disco integrate` now checks for the canonical splice junction
motif: ..]GT..->..AG[.. and returns edit distance + motif
2018-08-03 Youri Hoogstrate v0.17.4
* Improved filter / classification
2018-05-16 Youri Hoogstrate v0.17.3
* Quicker + tqdm() + certain hard/softclips per base are different
if this involves edges from/to different chromosomes + order
of lines in output file may change if score and entropy are
identical
2018-05-16 Youri Hoogstrate v0.17.2
* Milder entropy filter
2018-05-15 Youri Hoogstrate v0.17.1
* Adds certain classification features and a filter to remove
possible artifacts.
2018-05-14 Youri Hoogstrate v0.17.0
* Skips certain alignments that are putative cross-hybridization
artifacts. Requires re-run of `dr-disco detect`.
2018-04-03 Youri Hoogstrate v0.16.3
* Fixes `SA:Z:` tags by swapping strand information with CIGAR and
by replacing chromosomes to `=` if they are the same. This will
solve prevent dissapearing pannels in IGV 2.4.1 - 2.4.10.
A backwards incompatibility fix has directly been implemented and
the changes do not affect the outcome and only improve
visualization.
2018-03-09 Youri Hoogstrate
* Trigger Exception in `dr-disco integrate` when position of break
is out of bound relative to `--fasta`.
2018-03-06 Youri Hoogstrate v0.16.2
* Improved classification based on outliers
2018-02-09 Youri Hoogstrate v0.16.1
* Improves filter for extremely high expressed exonic fusions
2018-02-01 Youri Hoogstrate v0.16.0
* Adds the exons before the break and exons after the break to the
integrate results. Remark that the offset to match an exon is
[-2,+2] because STAR may introduce slight offset errors.
* Fixes bug in integrate where rather similar fusions in opposite
strands were still bundled together.
2018-02-01 Youri Hoogstrate v0.15.2
* Makes mismatches per base classification more stringent
unless `--ffpe` is used. Using `--ffpe` the old behaviour
is preserved.
2018-01-25 Youri Hoogstrate v0.15.1
* Added filter lr/intercept
2018-01-09 Youri Hoogstrate v0.15.0
* Bugfix resulting in higher number of detected frame shifts
* `dr-disco integrate --fasta <fa file>` provides edit distance to
canonical splice junction motif (quick impementation)
2017-12-20 Youri Hoogstrate v0.14.6
* New improvement to entropy filter
2017-12-20 Youri Hoogstrate v0.14.5
* Updated max clipping filter and entropy cutoff based
on previously misclassified datapoints
2017-12-18 Youri Hoogstrate v0.14.4
* Improvement to manymuts and entropy filter for score
values that are extremely large (>~700) which are
estimated using non interpolated datapoints
2017-11-20 Youri Hoogstrate v0.14.3
* Bugfix in filter (rounding error) causing unneccessary
n_split misclassifications
2017-11-20 Youri Hoogstrate v0.14.2
* Gzip support for `dr-disco classify`'s input files
2017-11-14 Youri Hoogstrate v0.14.1
* Update blacklist after analysis on misclassied entries
2017-10-27 Youri Hoogstrate v0.14.0
* Adds classification variable that determines minimum
alignment length on both sides of the junction
(--min_chim_overhang 50)
2017-10-26 Youri Hoogstrate v0.13.0
* Improved classification for exonic / spliced
* Added more stuff to blacklist (after analysing DNA seq)
2017-10-17 Youri Hoogstrate v0.12.2
* Typo in output (disregulation->dys...)
2017-10-27 Youri Hoogstrate v0.12.1
* Added more regions and junctions to blacklist
* Works around a STAR bug (assigning negative AS values)
2017-09-27 Youri Hoogstrate v0.12.0
* Added new classification variable focussing on fusions
with low number of reads
2017-09-27 Youri Hoogstrate v0.11.2
* Added many regions to the blacklist (based on repeat regions)
2017-09-26 Youri Hoogstrate v0.11.1
* Added many junctions to the blacklist (based on repeat regions)
2017-09-22 Youri Hoogstrate v0.11.0
* Added way to use mismatches + alignment score for classification
2017-09-08 Youri Hoogstrate v0.10.0
* Improved frameshift detection by looking for all split junctions
the data structure
* Added support and column for finding 'full gene dysregulation'
fusion transcripts
2017-07-26 Youri Hoogstrate v0.9.0
* Support for frame shift detection in Integrate function
* Some bugfixes in integrate
2017-07-05 Youri Hoogstrate v0.8.2
* Changed another filter, reduces the amount of false negatives
2017-07-05 Youri Hoogstrate v0.8.1
* Looser settings and new shape for entropy filter
2017-06-22 Youri Hoogstrate v0.8.0
* Adds `dr-disco integrate` to find genomic breaks and exon-to-
exon fused splice junctions that belong to the same event
* Adds donor acceptor calculation
* Adds possibility to add gene names by adding a GTF file
2017-06-16 Youri Hoogstrate v0.7.1
* Allows running `dr-disco fix` in parallel mode (random tmp files)
* Classified on slope
* Many new entries in blacklists
2017-05-17 Youri Hoogstrate v0.7.0
* Changed CLI interface
* Added `dr-disco classify`
* Removed classification step from `dr-disco detect` such that
classification can be done without re-running detect completely.
* Added blacklist system plus a few known contaminants
* Fixed broken nose (dependency)
* Adds some extra variables useful for classification
* Improved the TP and FP ratio of the filter
2017-04-12 Youri Hoogstrate v0.6.0
* Changed behavior of pruning: less post-merging steps necessary
* Added two extra variables that can be used for classification
2017-04-05 Youri Hoogstrate v0.5.0
* Large improvements in parsing junctions from reads and much better
performance on circRNAs
2017-03-23 Youri Hoogstrate v0.4.0
* Adds column indicating whether a result is likely to be circRNA
* Adds column with genomic distance between breakpoints
2017-03-13 Youri Hoogstrate v0.3.5
* Using shutil.move over os.rename (http://bugs.python.org/issue14848)
2017-03-02 Youri Hoogstrate v0.3.4
* Better way of handling stdio / logging for bioconda compatibility
2017-02-08 Youri Hoogstrate v0.3.3
* Huge improvement in performance in `extract subnetworks` by translating
a recursion problem into an iterative linear problem.
2017-02-03 Youri Hoogstrate v0.3.2
* Allows to run `dr-disco bam-extract` on non 'fixed' BAM-files
plus corresponding test cases
2017-02-01 Youri Hoogstrate v0.3.1
* Fix in bam fixing code for reads annotated with identical SA-tags
2017-01-30 Youri Hoogstrate v0.3.0
* Changes in CLI interface
2016-12-22 Youri Hoogstrate v0.2.0
* Rewritten large parts of the code
Improved classification system
Added argument (-m) allowing a trade-off between sensitivity and time
2016-11-13 Youri Hoogstrate v0.1.0
* Rewritten rejoin_splice_junctions resulting in a huge performance
increase. Rewritten and improved
extract_subnetworks_by_splice_junctions. Added test cases that
earlier failed in the development phase because of complex race
conditions. Using enum datatypes for Edge-types to improve memory
consumption. Added __lt__ function to quickly compare based on
genomic positions as hashes. Indexing and sorting is now also
based on this. Use xranges of ranges to improve performance.
2016-11-08 Youri Hoogstrate v0.0.10
* Uses HTSeq library as genomic index which improves performance.
Other speed improvements.
2016-11-02 Youri Hoogstrate v0.0.9
* Fixes critical race condition in extracting subnetworks with Edges that
are also splice junctions.
2016-11-01 Youri Hoogstrate v0.0.8
* Output includes columns containing the number of splice junctions
2016-10-31 Youri Hoogstrate v0.0.7
* Fixed a few small flaws in pruning (taking an alignment mistake
offset of 3bp into account and pruning nodes an identical l-position
2016-10-28 Youri Hoogstrate v0.0.6
* Better order in final output file
2016-10-27 Youri Hoogstrate v0.0.5
* Uses a single index structure for accessing all edges in a sorted
manner in order to improve the speed of pruning
2016-10-26 Youri Hoogstrate v0.0.4
* Total distance in pruning (sum of two sides) may not be more than
the insert size
2016-10-15 Youri Hoogstrate v0.0.3
* Improved extract_subnetworks to extracting only by splice junctions
Traversing is now limited on the insert size
2016-07-25 Youri Hoogstrate
* Improved pruning system in many ways and fixed special behaviour for
spanning_singleton_1/2 by adding spanning_singleton_1/2_r because
half of those were in the opposite strand. The HI-tag was used to
correct for this.
2016-06-15 Youri Hoogstrate v0.0.2
* fix-chimeric makes a destinction between spanning_paired_1 and spanning_paired_2
depending on wether it was the first or second chunk of the broken/split read.
This is also implemented for spanning_singleton_1/2.
2016-06-15 Youri Hoogstrate v0.0.1
* First working prototype with setup tools for fix-chimeric