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Merge 1.1.0-beta.2 #16

Merged
merged 63 commits into from
Feb 15, 2024
Merged

Merge 1.1.0-beta.2 #16

merged 63 commits into from
Feb 15, 2024

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@bepoli bepoli commented Feb 15, 2024

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bepoli and others added 30 commits August 26, 2023 17:13
@bepoli
add read_id to mappings file
0678585
@bepoli
add network.py
11a9ad9
@bepoli
add em.py
a4de527
@bepoli
add help to split_bc
55cbbf3
@bepoli
group features of multimapping read
fe034cf
@bepoli
Revert "add network.py"
7ac997a 
This reverts commit 11a9ad9.
@bepoli
new count strategy
6116398
@bepoli
[fix] 0 sorting threads
87d4d7e
@bepoli
bug fixes
bf52e65
@bepoli
use full TE name as feature ID
6b49c30
@bepoli
[fix] solve some obscure graph config
1b2f3b0
@bepoli
add networkx as dependency
d1eec20
@bepoli
get EM counts after uniques
23118ae
@bepoli
give priority to parent's node features
ab9646b
@bepoli
[fix] update variable names
a81c347
@bepoli
tag EM build 1.0.0-alpha.1
ad17d5f
@bepoli
Make all counts floats
ac1d6f6
@bepoli
[fix] remove empty features from EM matrix
3d44897
@bepoli
do not write counts less than 0.001
677b172
@bepoli
add logging
79d6275
@bepoli
vbump
ec1f702
@bepoli
replace ~ with # as name separator
101d115
@bepoli
[fix] get total number of features
8433fde
@bepoli
update bed reference
bbccdd1
@bepoli
update checksums
84d4fb4
@bepoli
bump
b2af17c
@bepoli
add back --dumpEC
3e07953
@bepoli
Merge pull request #1 from bepoli/em
cc1c049 
EM-based quantification
@bepoli
add comment
ec514b2
@bepoli
add manual dependency install instructions
e010ae9
bepoli added 25 commits November 9, 2023 14:33
@bepoli
print message between steps
f410dac
@bepoli
add more logging
fa455d9
@bepoli
decode cell barcode during logging
d24a3a0
@bepoli
add verbose to cell count logging
0b149bd
@bepoli
optimize EM speed
4940f89
@bepoli
[fix] features list out of range in bidirected subgraphs
ee4c99c
@bepoli
open dump file only once
9722e10
@bepoli
[fix] do not close dump file if no --dumpEC
1194c6b
@bepoli
connect_umis slightly faster
1c204a5
@bepoli
optimize graph building speed
ca252ce
@bepoli
update md5sum for ec_dump.tsv.gz
c3ba4b7
@bepoli
optimize memory usage when adding edges to graph
9114c03
@bepoli
optimize permutation speed
c572d4e
@bepoli
better syntax and comments
a23127e
@bepoli
remove unused code
782361a
@bepoli
new output directory structure
5d57dea
@bepoli
bump
ee3acb7
@bepoli
updated readme for 1.1.0
c7efcdb
@bepoli
[fix] missing column name in ec_dump.tsv
f4655a4
@bepoli
sort ec_dump file correctly
820d475
@bepoli
update md5sum
5377346
@bepoli
fix third party code
774d8f3
@bepoli
update license year
35406a3
@bepoli
bump 1.1.0-beta.2
ba66a20
@bepoli
code cleanup
995d00a
@bepoli bepoli added the enhancement New feature or request label Feb 15, 2024
@bepoli bepoli added this to the v1.1.0 milestone Feb 15, 2024
@bepoli bepoli self-assigned this Feb 15, 2024
@bepoli bepoli merged commit 9224900 into main Feb 15, 2024
1 check passed
@bepoli bepoli deleted the dev branch February 15, 2024 09:35
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