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broadinstitute
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longbow
Annotation and segmentation of MAS-seq data
https://broadinstitute.github.io/longbow/
BSD 3-Clause "New" or "Revised" License
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Issues with 'annotate' and 16-element arrays
#208
hdm-23
opened
1 year ago
0
ModuleNotFoundError: No module named 'ordered_set'
#207
xuxia10
opened
1 year ago
1
Installation conundrum
#206
phpeters
closed
1 year ago
2
TypeError: create_simple_split_array_element() missing 1 required positional argument: 'split_read_index'
#205
ashokpatowary
closed
1 year ago
0
rebuild HMM inside subprocesses
#204
jamestwebber
closed
1 year ago
0
moved load_model to allow stream processing
#203
jamestwebber
opened
1 year ago
0
Updated python version
#202
jamestwebber
opened
1 year ago
0
allow "longbow inspect" from file of read names
#201
jamestwebber
opened
1 year ago
0
move models to JSON files
#200
jamestwebber
opened
1 year ago
1
pysam output issue
#199
voyn
opened
1 year ago
4
removed unused imports, fixed f-strings, etc
#198
jamestwebber
closed
1 year ago
0
stream read less than specified amount, expected 4, found 0
#197
TinyTasy
opened
1 year ago
2
Some minor fixes
#196
kvg
closed
1 year ago
0
New documentation on custom Longbow models.
#195
kvg
closed
1 year ago
0
Kvg mas16
#194
kvg
closed
2 years ago
0
Can Longbow segment libraries using alternatives to the 10X 5' and 3' sequences?
#193
claumer
closed
1 year ago
2
let inspect command read from stdin
#192
jamestwebber
closed
2 years ago
1
Confusion over longbow correct
#191
sagnikbanerjee15
closed
2 years ago
2
random segment extraction no longer an option?
#190
morellr
opened
2 years ago
1
Fixing a bug that caused `correct_umi` to fail on unaligned bams.
#189
jonn-smith
closed
2 years ago
0
Exposed the back alignment score parameter in `correct_umi`
#188
jonn-smith
closed
2 years ago
0
How to get barcode and umi file after extract step ?
#187
hmyh1202
closed
1 year ago
2
Fixed all potential divide by 0 errors in logging.
#186
jonn-smith
closed
2 years ago
0
Updated `correct_umi` with some additional features.
#185
jonn-smith
closed
2 years ago
0
Exposed more `correct_umi` parameters
#184
jonn-smith
closed
2 years ago
0
get_segments(...) now returns three things rather than two
#183
kvg
closed
2 years ago
0
Add a pseudocount for num_reads to prevent a rare divide-by-zero error
#182
kvg
closed
2 years ago
0
Fix parsing of zero-length segments
#181
kvg
closed
2 years ago
0
Fixed bug with collapse annotations wherein the length of the first a…
#180
kvg
closed
2 years ago
1
Kvg minor fixes for sim
#179
kvg
closed
2 years ago
0
`tagfix` does not update the cigar tag
#178
jonn-smith
opened
2 years ago
0
New segment cigars need to be refactored
#177
jonn-smith
opened
2 years ago
0
`models --dump` graph `png` output needs a better layout algorithm.
#176
jonn-smith
opened
2 years ago
0
New `models` command no longer dumps all file formats of models to disk.
#175
jonn-smith
opened
2 years ago
0
Move to `.sam` files for all test data
#174
jonn-smith
opened
2 years ago
0
Kvg hierarchical models
#173
kvg
closed
2 years ago
0
Added `umi_correct` tool.
#172
jonn-smith
closed
2 years ago
0
`XQ` tag has an off-by-one error in its calculations
#171
jonn-smith
opened
2 years ago
0
documentation on how to create new models
#170
krobison13
opened
2 years ago
2
bump python req
#169
jamestwebber
closed
2 years ago
0
pass bam header as dict for subprocesses
#168
jamestwebber
closed
2 years ago
0
fix syntaxwarning in python 3.8: `is not ""` is not recommended
#167
jamestwebber
closed
2 years ago
1
bump python requirement to <3.8
#166
jamestwebber
closed
2 years ago
3
Refactor tests to be more independent
#165
jamestwebber
closed
2 years ago
0
We need to store the segments that `sift` generates in a new tag in the reads (NOT the `sg` tag).
#164
jonn-smith
opened
2 years ago
0
fixed various bugs and tests
#163
jamestwebber
closed
2 years ago
0
Add warning to `correct` if the user is using more than 1 thread.
#162
jonn-smith
opened
2 years ago
0
3' model UMI should be changed to 12 bases for latest 10x kits
#161
jonn-smith
closed
2 years ago
2
Fixed 10x3p model UMI length and added extra progress printing
#160
jonn-smith
closed
2 years ago
0
tweaked how subcommands were added at runtime
#159
jamestwebber
closed
2 years ago
0
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