svviz/svviz issues and pull requests

#55 - Input format of a complex SV

Issue - State: open - Opened by z65263299 about 1 month ago

#54 - Can variant-supporting reads be saved?

Issue - State: closed - Opened by teng-gao about 6 years ago - 1 comment

#53 - Would it be possible to add --ip as an option for the server?

Issue - State: open - Opened by Karhide over 6 years ago - 2 comments

#52 - svviz doesn't seem to honor `--processes`

Issue - State: closed - Opened by ifiddes-10x-zz over 6 years ago - 4 comments

#51 - svviz demo can't parse answer to download prompt

Issue - State: closed - Opened by 0xaf1f about 7 years ago - 2 comments

#50 - AttributeError: 'module' object has no attribute 'AlignmentFile'

Issue - State: closed - Opened by YiweiNiu about 7 years ago - 3 comments

#49 - Cannot load demo (OSX)

Issue - State: closed - Opened by ranasats over 7 years ago - 2 comments

#48 - svviz installation Ubuntu

Issue - State: closed - Opened by mitul-patel over 7 years ago - 1 comment

#47 - ref vs alt dotplots

Issue - State: closed - Opened by nspies over 7 years ago - 1 comment
Labels: enhancement

#46 - problems installing on Cygwin

Issue - State: closed - Opened by pcantalupo almost 8 years ago - 1 comment

#45 - uninstall

Issue - State: closed - Opened by rcastil almost 8 years ago - 2 comments

#44 - Unprotected None objects

Issue - State: closed - Opened by sandoro about 8 years ago - 4 comments

#43 - AssertionError in svviz

Issue - State: closed - Opened by sandoro about 8 years ago - 4 comments

#42 - 'module' object has no attribute 'SafeFunction'

Issue - State: closed - Opened by fritzsedlazeck about 8 years ago - 2 comments

#41 - multiprocessing broken with latest version of joblib

Issue - State: closed - Opened by nspies about 8 years ago - 1 comment
Labels: bug

#40 - more documentation.

Issue - State: closed - Opened by zeeev over 8 years ago - 4 comments
Labels: documentation

#39 - Output insert size distributions as pdf in batch mode

Issue - State: closed - Opened by jzook over 8 years ago

#38 - Output stats as they're generated during batch mode?

Issue - State: closed - Opened by jzook over 8 years ago - 3 comments

#37 - Orientation override and orientation for breakpoint spanning reads.

Issue - State: closed - Opened by nh13 over 8 years ago - 1 comment

#36 - Help message should include all event types

Issue - State: closed - Opened by nh13 over 8 years ago - 4 comments
Labels: documentation

#35 - Pacbio analysis gets stuck "forever" at close to 100%

Issue - State: closed - Opened by jzook almost 9 years ago - 8 comments
Labels: bug

#34 - --min-reads

Issue - State: closed - Opened by jzook almost 9 years ago - 1 comment

#33 - Add support for dotplots when using export

Issue - State: closed - Opened by nspies almost 9 years ago - 1 comment
Labels: enhancement

#32 - timeout error in batch mode producing pdf

Issue - State: closed - Opened by jzook almost 9 years ago - 4 comments

#31 - Better warning when reference fasta is not provided

Issue - State: closed - Opened by nspies almost 9 years ago
Labels: bug

#30 - Improve flanking reads view of pacbio data

Issue - State: closed - Opened by nspies almost 9 years ago
Labels: enhancement

#29 - Add utility to estimate aln-quality for pacbio datasets

Issue - State: closed - Opened by nspies almost 9 years ago
Labels: enhancement

#28 - how to specify the strandness when visualize translocations

Issue - State: closed - Opened by crazyhottommy almost 9 years ago - 7 comments

#27 - Actually enable dotplots for multi-part variants

Pull Request - State: closed - Opened by apregier almost 9 years ago - 1 comment

#26 - Describe multi-part events better

Issue - State: closed - Opened by nspies almost 9 years ago - 1 comment

#25 - --pair-min-mapq should be applied to reads within the original search regions

Issue - State: closed - Opened by nspies almost 9 years ago - 1 comment
Labels: bug

#24 - Document large event handling

Issue - State: closed - Opened by nspies almost 9 years ago - 1 comment
Labels: documentation

#23 - If args.format is defined, don't require file suffix

Pull Request - State: closed - Opened by apregier almost 9 years ago

#22 - Print realignment progress even when not in tty

Issue - State: closed - Opened by nspies almost 9 years ago
Labels: enhancement

#21 - Handling for multiple bam files with the same name

Issue - State: closed - Opened by nspies almost 9 years ago - 1 comment

#20 - Add option to convert deletions to breakend format

Issue - State: closed - Opened by nspies almost 9 years ago - 2 comments
Labels: enhancement

#19 - Add a --max-size option

Issue - State: closed - Opened by nspies almost 9 years ago - 1 comment
Labels: enhancement

#18 - Loading reads should bail early if possible if --max-reads is set

Issue - State: closed - Opened by nspies almost 9 years ago - 2 comments
Labels: enhancement

#17 - svviz crashes after not being able to find reads for certain SV events

Issue - State: closed - Opened by rpadmanabhan almost 9 years ago - 11 comments

#16 - svviz seems to take a lot of time on some SV's

Issue - State: closed - Opened by gatoravi about 9 years ago - 28 comments

#15 - Fix warning message

Pull Request - State: closed - Opened by gatoravi about 9 years ago

#14 - Breakpoints don't line up across axis and data tracks in export

Issue - State: closed - Opened by nspies over 9 years ago
Labels: bug

#13 - option to export visualizations (PDF/SVG/PNG) in batch mode

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: someday

#12 - exclude ambiguous reads outside breakpoints

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment

#11 - Output additional statistics about ref, alt, and ambiguous reads

Issue - State: closed - Opened by jzook over 9 years ago - 1 comment
Labels: enhancement

#10 - Include javascript and css components

Issue - State: closed - Opened by nspies over 9 years ago
Labels: bug

#9 - Merge adjacent segments

Issue - State: closed - Opened by nspies over 9 years ago
Labels: bug

#8 - Create insert size distribution plots using plain rpy2

Issue - State: closed - Opened by nspies over 9 years ago
Labels: enhancement

#7 - Calculate alignment score distribution from input bam

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: someday

#6 - Submit to pypi

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: distribution

#5 - Arbitrary breakpoint handling

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: enhancement

#4 - Translocations

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: someday

#3 - Batch analysis

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: enhancement

#2 - VCF parsing

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: enhancement

#1 - Infer orientation from input data

Issue - State: closed - Opened by nspies over 9 years ago - 1 comment
Labels: enhancement

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