Change log¶
1.6.2¶
fixed a regression that prevented the demo from being run from python2
1.6.1¶
minor tweaks
1.6.0¶
Adds support for python 3.x (python 2.7 will continue to be supported as well).
1.5.2¶
Improvements:
- added an option
--export-insert-sizes
which exports the insert size distribution plots to png files, one per event per sample. - added better warning and error messages around command line arguments
- output progress every 30 seconds when not in an interactive shell (eg stderr redirected to file)
- demo data is now downloaded from github
1.5.1¶
Improvements:
- now supports
<TRA>
-style translocations - added a new
--sample-reads
option that can be used to downsample reads (read pairs) – use with caution!
Bugfixes:
- removed joblib dependency (joblib 0.10 introduced some API changes that were not compatible with svviz)
1.5.0¶
Improvements:
- dotplots can now be written to file when in export mode
- added an optional wrapper around the re-alignment module, allowing processing of long-read (eg pacbio) data despite a buggy Smith-Waterman library; specify
--processes -1
to enable this mode - added
--aln-score-delta
option to allow specifying how different the ref and alt alignments must be in order to choose one over the other (rather than punting the read to ambiguous); this option allows specifying a fraction, which can be useful for sequencing libraries such as pacbio with reads of differing lengths
Bugfixes:
- corrected help messages for structural variant formats
1.4.0¶
This release includes many small improvements and bugfixes.
One change to svviz’s behavior is notable:
- the
--pair-min-mapq
option now requires one read end to both exceed this mapq threshold and be near the variant
Improvements:
- implemented a largedeletion variant type, with an option to automatically convert deletions above a certain size to use “breakend” mode, thus only analyzing reads near the deletion breakpoints (see the FAQ)
- implemented a
--max-size
option which skips variants exceeding the specified number of nucleotides (see the FAQ) - when the
--max-reads
option is provided in batch mode, svviz should stop analyzing a variant much sooner if that variant exceeds the max-reads threshold - dotplots now work with multi-part variants such as breakends
- better conversion between chromosome formats (chrX<->X)
- many tweaks to the progress information provided as svviz is running
- no longer require file suffix on
--export
when in batch mode and--format
is specified (A. Regier) - added support for using inkscape for PDF export; the
--converter
option can be used to choose between different conversion software packages - the test suite is now mostly included in the git repository in case anyone else wants to run the regression tests
- added demo 3, a deletion with an example annotation track
Bugfixes: - fixed handling of variant breakpoints near the ends of chromosomes (rpadmanabhan) - fixed a bug where reads mapping to both strands with similar alignment scores might not have been marked as multimapping - fixed a bug which prevented correctly analyzing translocations on the same chromosome on the same strand
1.3.2¶
This release includes a number of bugfixes and additions to the documentation.
- bed annotations should now work again (C. Lee)
- added support for gff files without gene or transcript IDs
- fixed support for
--processor 1
(A. Ramu) - added more information about the “lots fo reads in region” warning (see FAQ)
1.3.1¶
This release adds substantial improvements to the handling of multi-mapping reads (ie those aligning to multiple locations near the structural variant). See here for more details.
1.3.0¶
This release adds a number of new features and fixes several bugs:
- added support for displaying gene models (exons and introns) from GFF-formatted annotation files
- added option to display reads that are in flanking genomic regions, providing context for a structural variant
- initial implementation of breakend support (note that, currently, the breakends must be distant from one another, and breakend support has not been implemented from vcf files yet)
- added checkbox to web interface to hide/show flanking reads
- added option to define the web server port, making it easier to use ssh tunneling to access svviz running on a server
- now auto-detect the number of cores available on a machine (used for the realignment step)
- added option to specify how many processes (cores) to use when performing realignment
- improved handling of paired-end reads that align to the same location
- added option to skip variants with very deep read coverage (typically indicative of a repetitive genomic region); useful in batch mode
1.2.0¶
This is a major feature release, implementing support for visualizing translocations.
Additional changes:
- does a better job finding reads to estimate empirical insert size distribution and read pair orientation
- checks that bam files have index and produce a more helpful error message if they do not
- annotations now also check to see if there’s a mismatch between “chrX” and “X” formats, and try to automatically fix it
- wrapping pyfaidx with a pickle-able
GenomeSource
object; should make automated debugging easier - added
--skip-cigar
option which disables visualizing mismatches and indels; this will speed up exporting and the web browser view for data with many errors (eg PacBio)
1.1.1¶
- no longer requires X11 if rpy2 is installed (I know, this was a weird one)
1.1.0¶
- code refactoring and new tests that should make it easier to modify and improve the visualizations produced by svviz
- added experimental support for webkitToPDF, a command-line tool that uses OS X’s built-in SVG support (part of Safari’s webpage rendering code) to convert SVGs to PDFs; this currently requires a separate install of webkitToPDF. webkitToPDF produces much better PDFs than rsvg-convert does (for example, fonts are converted properly)
1.0.9¶
- added link to preprint on bioRxiv
- added support for exporting one pdf per event in batch mode
- tweaks and fixes for visualizations
- changed coloring of insertions in reads to cyan
1.0.8¶
- filter out reads that align multiple times within the region of the structural variant (“multimapping”)
- many minor bug-fixes and interface tweaks
1.0.7¶
- demo data now gets downloaded from Stanford webspace
- added
--version
command line option - no longer fails if pandas is an older version
- check for librsvg before we do the analysis
1.0.6¶
- fixed bug that prevented
--export
option from working - ref and alt alignment scores must differ by at least 2 in order to assign a read to an allele by alignmentScore
- minor bug fixes
1.0.5¶
- implemented batch mode to analyze multiple variants at once