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andersen-lab
/
ivar
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
https://andersen-lab.github.io/ivar/html/
GNU General Public License v3.0
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Change codon and its translation to match CDS direction in GFF
#181
asereewit
closed
1 month ago
3
Incorrect amino acid numbering
#180
proychou
closed
3 weeks ago
7
weird variant TSV output
#179
Norina28
opened
2 months ago
1
header format of .tsv did not match!
#178
zdk427
opened
2 months ago
3
Does ivar trim only from the ends of aligned BAM files?
#177
yl315504
opened
2 months ago
2
Cmake
#176
cmaceves
closed
3 months ago
0
iVAR inappropriately shifts position of reverse mapped reads for ONT data
#175
Alan-Collins
closed
3 weeks ago
13
Parsing GFF_FEATURE
#174
jfouret
opened
3 months ago
0
Variants returns multiple AA with 1.00 frequency
#173
shoulton-invivyd
opened
5 months ago
2
REF_AA not consistent with actual AA at the position from reference protein fasta file
#172
Shawn-X-Zhang
opened
5 months ago
2
Header format error in ivar filtervariants
#171
fshepherd13
opened
7 months ago
1
Segmentation fault (core dumped)
#170
mksingh2104
opened
11 months ago
5
fix build failure with gcc-13
#169
emollier
opened
11 months ago
1
Issue 162
#168
cmaceves
opened
1 year ago
0
Discrepancy between samtools depth and TOTAL_DEPTH in ivar
#167
Paururo
closed
6 months ago
1
Update Dockerfile htslib version and ubuntu version
#166
cmaceves
closed
1 year ago
0
Error building the docker image from the Dockerfile
#165
jonbra
closed
1 year ago
3
iVar variants weird output
#164
sejmodha
closed
2 months ago
5
clarification of ivar trim -e option
#163
sgsutcliffe
closed
1 year ago
1
Further speedup in iVar Trim primer finding
#162
niemasd
opened
1 year ago
3
update ubuntu images
#161
cmaceves
closed
1 year ago
0
fix for ivar trim hanging with -f parameter
#160
cmaceves
closed
1 year ago
0
ivar trim hangs when using -f parameter
#159
cmaceves
closed
1 year ago
0
Fix for problem with combined use of stdin and -m parameter
#158
cmaceves
closed
1 year ago
0
ivar trim -f option incompatible with new piping functionality
#157
wm75
closed
1 year ago
3
Issue 143
#156
cmaceves
closed
1 year ago
0
Updating for the acceptance of stdin
#155
cmaceves
closed
1 year ago
0
slow performance of ivar 1.3.2
#154
pdp10
closed
1 year ago
1
Issue 143
#153
cmaceves
closed
1 year ago
0
changing type of min_depth from uint8_t to uint32_t
#152
cmaceves
closed
1 year ago
0
Issue 147
#151
cmaceves
closed
1 year ago
2
Bump version number to 1.3.2
#150
khyox
closed
1 year ago
1
Clarification of new ivar consensus -c (minimum insertion frequency) parameter
#149
wm75
opened
1 year ago
0
ivar version command not updated accordingly
#148
hsnguyen
closed
1 year ago
0
Remove excess calls to insertionSort
#147
cmaceves
closed
1 year ago
3
Solving compile errors for macos
#146
cmaceves
closed
1 year ago
0
Silent integer overflows in several ivar params
#145
wm75
closed
1 year ago
0
Use samtools mpileup -a option in consensus pipeline
#144
wm75
opened
1 year ago
0
Automated minimum read length "-m" setting
#143
joshuailevy
closed
1 year ago
2
Ivar-Freyja Pipeline creates +/- bases and "#Name?" cells
#142
EESI-jv545
closed
1 year ago
1
Fix compilation on newer gcc versions
#141
JacobHayes
closed
1 year ago
2
Contamination detection feature
#140
cmaceves
closed
8 months ago
0
Concurrency for `ivar trim`?
#139
philiptzou
opened
1 year ago
10
Extended io for ivar trim
#138
ashwinbabu888
closed
1 year ago
1
addressing issue #132
#137
cmaceves
closed
1 year ago
4
call_consensus_pileup.h: fix build failure with Gcc 12
#136
emollier
closed
1 year ago
1
fix GCC 10 compile issue [-Werror=mismatched-new-delete]
#135
fizwit
closed
1 year ago
3
build from source fails with GCC >= 10
#134
fizwit
closed
1 year ago
1
Please update release
#133
fizwit
closed
1 year ago
2
primer trimming issue with small insert sizes
#132
cmaceves
closed
1 year ago
0
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