nspies svviz2 issues - Githubissues

nspies / svviz2

for visual evaluation of read support for structural variation

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issues

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Update kde.py

#70 jgarces02 closed 5 months ago
1
AttributeError: module 'numpy' has no attribute 'float' [bug]

#69 jgarces02 opened 6 months ago
1
specify that installation is incompatible with cython 3+

#68 nspies closed 1 year ago
0
git hangs when installing via the default install instruction

#67 pwaltman closed 1 year ago
9
Remapping long reads with minimap2 or NGMLR

#66 JYLeeBioinfo opened 3 years ago
1
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 moldach opened 4 years ago
10
move scipy.misc.comb import to scipy.special.comb

#64 nspies closed 4 years ago
0
AttributeError: module 'scipy.misc' has no attribute 'comb'

#63 ehenrion closed 4 years ago
1
TypeError: __init__() got multiple values for argument 'name'

#62 moldach closed 4 years ago
4
WARNING - SKIPPING VARIANT about INS

#61 dxkeac opened 5 years ago
0
Installation issue

#60 ObliviousMonkey closed 3 years ago
2
Parser vcf

#59 danielavarelat opened 5 years ago
1
Installation failing for zlib.h not found

#58 MaestSi closed 5 years ago
3
Annotation track

#57 abrusell opened 6 years ago
1
ssw not available

#56 frankbioinfo closed 5 years ago
7
Documentation

#55 nspies opened 6 years ago
0
Labeling large insertions

#54 jzook opened 6 years ago
7
Figure out what to do with reads internal to an event

#53 nspies opened 6 years ago
0
Allow fully sequence-defined events to skip SVTYPE

#52 maiziex closed 6 years ago
1
Better handling of events with missing ID

#51 maiziex closed 6 years ago
0
Separating counts by haplotype

#50 jzook closed 6 years ago
4
UnboundLocalError: local variable 'exportData' referenced before assignment

#49 ifiddes-10x-zz closed 6 years ago
3
AttributeError: 'str' object has no attribute 'start

#48 ifiddes-10x-zz closed 6 years ago
1
Better handling of supplementary alignments

#47 nspies closed 6 years ago
0
Calculate which reads overlap unique regions

#46 nspies opened 6 years ago
0
Add number of inserted bases to visualization

#45 jzook closed 6 years ago
1
RuntimeWarning: invalid value encountered in subtract scores = scores - best_score

#44 jzook closed 7 years ago
1
Name of bam file missing to separate reads in pdf

#43 jzook closed 7 years ago
1
Reporting of n_mismatch and n_indel is lower than in the image for PacBio

#42 jzook closed 6 years ago
1
Reimplement visualizating tandem repeats

#41 nspies closed 7 years ago
1
Make sure all breakpoints are visualized even when reads don't overlap

#40 nspies closed 7 years ago
2
Use REF and ALT for all sequence-defined variants

#39 jzook closed 7 years ago
1
Add indexes to more annotations in the tsv that have coordinates

#38 jzook closed 6 years ago
2
Add read vs REF and read vs ALT dotplots

#37 amwenger closed 7 years ago
1
Use same basepair:pixel ratio for X and Y in dotplots

#36 amwenger closed 7 years ago
0
Failed Python import of _mapq

#35 amwenger closed 7 years ago
5
Support for parsing of more SV types from VCF

#34 nspies opened 7 years ago
0
update dotplots

#33 nspies closed 7 years ago
0
genosv hangs while tallying quick consensus

#32 jzook closed 7 years ago
0
Adjustments to report

#31 nspies closed 7 years ago
1
error finding temp amb bam file

#30 jzook closed 7 years ago
1
Use trf as the tandem repeat finder, if present

#29 nspies closed 7 years ago
0
Count reads fully spanning tandem repeats

#28 jzook opened 7 years ago
1
additional annotations for ambiguous reads

#27 jzook closed 7 years ago
0
Dotplots should show a fixed window around the breakpoints

#26 nspies closed 7 years ago
0
Better handling of assembled contigs as input

#25 nspies opened 7 years ago
1
change x-axis ticks when using --also-plot-context

#24 jzook closed 7 years ago
1
Dotplots

#23 nspies closed 7 years ago
0
Fix chromosome chrNN/NN formatting compatibility issues

#22 nspies closed 7 years ago
0
Clean up logging output

#21 nspies closed 7 years ago
1