nspies/svviz2

Issues

• AttributeError: module 'numpy' has no attribute 'float' [bug]

  #69 opened 4 months ago by jgarces02
  1

• git hangs when installing via the default install instruction

  #67 opened a year ago by pwaltman
  9

• ERROR:root:Unable to load cythonized quickconsensus module; this is likely because pysam has been updated since genomeview was originally install. To fix this, force reinstall genomeview: pip install --upgrade --force-reinstall genomeview

  #65 opened 4 years ago by moldach
  10

• Remapping long reads with minimap2 or NGMLR

  #66 opened 3 years ago by hd00ljy
  0

• Installation issue

  #60 opened 3 years ago by ObliviousMonkey
  2

• TypeError: __init__() got multiple values for argument 'name'

  #62 opened 4 years ago by moldach
  4

• AttributeError: module 'scipy.misc' has no attribute 'comb'

  #63 opened 4 years ago by ehenrion
  1

• WARNING - SKIPPING VARIANT about INS

  #61 opened 5 years ago by dxkeac
  0

• Parser vcf

  #59 opened 5 years ago by danielavarelat
  1

• Installation failing for zlib.h not found

  #58 opened 6 years ago by MaestSi
  3

• ssw not available

  #56 opened 6 years ago by frankbioinfo
  7

• Annotation track

  #57 opened 6 years ago by abrusell
  1

• Labeling large insertions

  #54 opened 6 years ago by jzook
  7

• Separating counts by haplotype

  #50 opened 6 years ago by jzook
  4

• Documentation

  #55 opened 6 years ago by nspies
  0

• Figure out what to do with reads internal to an event

  #53 opened 6 years ago by nspies
  0

• Reporting of n_mismatch and n_indel is lower than in the image for PacBio

  #42 opened 6 years ago by jzook
  1

• Better handling of supplementary alignments

  #47 opened 6 years ago by nspies
  0

• Better handling of events with missing ID

  #51 opened 6 years ago by maiziex
  0

• Allow fully sequence-defined events to skip SVTYPE

  #52 opened 6 years ago by maiziex
  1

• UnboundLocalError: local variable 'exportData' referenced before assignment

  #49 opened 7 years ago by ifiddes-10x-zz
  3

• AttributeError: 'str' object has no attribute 'start

  #48 opened 7 years ago by ifiddes-10x-zz
  1

• Calculate which reads overlap unique regions

  #46 opened 7 years ago by nspies
  0

• Add number of inserted bases to visualization

  #45 opened 7 years ago by jzook
  1

• Add indexes to more annotations in the tsv that have coordinates

  #38 opened 7 years ago by jzook
  2

• Add read vs REF and read vs ALT dotplots

  #37 opened 7 years ago by amwenger
  1

• Make sure all breakpoints are visualized even when reads don't overlap

  #40 opened 7 years ago by nspies
  2

• Name of bam file missing to separate reads in pdf

  #43 opened 7 years ago by jzook
  1

• RuntimeWarning: invalid value encountered in subtract scores = scores - best_score

  #44 opened 7 years ago by jzook
  1

• Reimplement visualizating tandem repeats

  #41 opened 7 years ago by nspies
  1

• Use REF and ALT for all sequence-defined variants

  #39 opened 7 years ago by jzook
  1

• Failed Python import of _mapq

  #35 opened 7 years ago by amwenger
  5

• Use same basepair:pixel ratio for X and Y in dotplots

  #36 opened 7 years ago by amwenger
  0

• Support for parsing of more SV types from VCF

  #34 opened 7 years ago by nspies
  0

• update dotplots

  #33 opened 7 years ago by nspies
  0

• Clean up logging output

  #21 opened 7 years ago by nspies
  1

• Better handling of assembled contigs as input

  #25 opened 7 years ago by nspies
  1

• change x-axis ticks when using --also-plot-context

  #24 opened 7 years ago by jzook
  1

• Count reads fully spanning tandem repeats

  #28 opened 7 years ago by jzook
  1

• Adjustments to report

  #31 opened 7 years ago by nspies
  1

• genosv hangs while tallying quick consensus

  #32 opened 7 years ago by jzook
  0

• error finding temp amb bam file

  #30 opened 7 years ago by jzook
  1

• additional annotations for ambiguous reads

  #27 opened 7 years ago by jzook
  0

• Use trf as the tandem repeat finder, if present

  #29 opened 7 years ago by nspies
  0

• Dotplots should show a fixed window around the breakpoints

  #26 opened 7 years ago by nspies
  0

• Fix chromosome chrNN/NN formatting compatibility issues

  #22 opened 7 years ago by nspies
  0

• Dotplots

  #23 opened 7 years ago by nspies
  0

• Improve handling of different alignment parameters for pacbio etc

  #18 opened 7 years ago by nspies
  6

• Sequence-resolved deletions should only have 2 segments

  #20 opened 7 years ago by nspies
  0

• Add option to set window size output in visualization

  #19 opened 7 years ago by jzook
  1