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).

1.5.3

Bugfixes:

• fixed an error with running demos

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