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5eb4b15
starting
Jul 30, 2025
70251f8
starting
Jul 30, 2025
c40f0ce
starting
Jul 30, 2025
8e76280
tests passing
Jul 30, 2025
4d7e2b7
update iterator for bam ranges
Jul 30, 2025
ee10e10
update name for bamranges
Jul 30, 2025
d86f270
this will be a major update
Jul 30, 2025
420daa1
fix?
Jul 31, 2025
a160aa5
fix?
Jul 31, 2025
c845d18
fix?
Jul 31, 2025
3f447c8
fix?
Jul 31, 2025
a9018c8
fix?
Jul 31, 2025
c23f282
fix?
Jul 31, 2025
efc3e39
fix?
Jul 31, 2025
17abd66
fix?
Jul 31, 2025
cae915c
fix?
Aug 1, 2025
603891f
fix?
Aug 1, 2025
e18d8b2
fix?
Aug 1, 2025
64d52b2
fix?
Aug 1, 2025
d7f6729
fmt
Aug 1, 2025
b3c14e1
inital inject subcommand structure
Aug 1, 2025
0ef6b34
keep order
Aug 1, 2025
93572d9
keep order
Aug 1, 2025
49dfd56
split long seq
Aug 4, 2025
9d2e782
split long seq
Aug 4, 2025
651495a
split long seq
Aug 4, 2025
2963e17
split long seq
Aug 4, 2025
aac80af
split long seq
Aug 4, 2025
7b73a32
split long seq
Aug 4, 2025
f3e915c
split long seq
Aug 4, 2025
efea8e4
Add a pg-pansn command to add pg contig names, and do dsa phasing.
Aug 5, 2025
106d6bc
Add uncompressed
Aug 5, 2025
e9fe4ce
rename
Aug 5, 2025
a0d2dfb
rename
Aug 5, 2025
33ff429
only check hardclipping if there is MM and ML tags
Aug 5, 2025
e5c74fd
only check hardclipping if there is MM and ML tags
Aug 5, 2025
bb4b82f
fix py-ft build
Aug 5, 2025
d013208
only check hardclipping if there is MM and ML tags
Aug 5, 2025
e2cbf13
drop hardclip
Aug 5, 2025
0f90b8b
tags
Aug 5, 2025
2834f2d
start bed tags
Aug 5, 2025
66ff116
add some tests
Aug 5, 2025
deac96c
first draft of injection and extraction from the BAM
Aug 6, 2025
2e89d06
first draft of fibertig that doesn't fail if beds spand a boarder
Aug 7, 2025
ab53ccb
Working version of fibertig, I think
Aug 11, 2025
efc0726
inject opts
Aug 13, 2025
761677c
clippy
Aug 13, 2025
4bf2523
adjust usage of mapq threshold
Aug 13, 2025
005f204
adjust usage of supp
Aug 13, 2025
50d25a8
put the bed header into the bam header if it is there
Aug 13, 2025
c977afe
clippy and format
Aug 13, 2025
b5ee883
fix doubles
Aug 19, 2025
7d01359
fix doubles
Aug 19, 2025
fcd1582
errors
Aug 19, 2025
fb058ad
errors
Aug 19, 2025
39b5740
errors
Aug 19, 2025
e3cec06
errors
Aug 19, 2025
8756303
errors
Aug 19, 2025
ee55059
errors
Aug 19, 2025
27b9beb
errors
Aug 19, 2025
ae9a4ce
errors
Aug 19, 2025
bf9b46f
simplify
Aug 20, 2025
18ecad9
simplify
Aug 20, 2025
7aab9b4
copy header
Aug 21, 2025
b8acd2b
copy header
Aug 21, 2025
d54acda
copy header
Aug 21, 2025
36505bb
add a function to deal with broken pipes
Aug 22, 2025
e3c0ee7
let inject do all the pansn things
Aug 22, 2025
2989f5d
start the pipeline
Aug 22, 2025
1fbfd4d
adding a data access page
Aug 22, 2025
6eeaec8
adding a data access page
Aug 23, 2025
09e57de
save a copy of the bam header if wanted
Aug 29, 2025
6c18e60
save a copy of the bam header if wanted
Aug 29, 2025
64b57d6
save a copy of the bam header if wanted
Aug 29, 2025
4cc88a7
save a copy of the bam header if wanted
Aug 29, 2025
ac8bba7
save a copy of the bam header if wanted
Aug 29, 2025
29b75cb
save a copy of the bam header if wanted
Aug 29, 2025
a914a02
save a copy of the bam header if wanted
Aug 29, 2025
eb6a9d5
save a copy of the bam header if wanted
Aug 29, 2025
a647ecf
save a copy of the bam header if wanted
Aug 29, 2025
38a909f
save a copy of the bam header if wanted
Aug 29, 2025
f69493f
save a copy of the bam header if wanted
Aug 29, 2025
559e6ec
save a copy of the bam header if wanted
Aug 29, 2025
a655931
save a copy of the bam header if wanted
Aug 29, 2025
29ef311
save a copy of the bam header if wanted
Aug 29, 2025
01aa25e
save a copy of the bam header if wanted
Aug 29, 2025
c441e71
save a copy of the bam header if wanted
Aug 29, 2025
6f80e92
save a copy of the bam header if wanted
Aug 29, 2025
3a65818
save a copy of the bam header if wanted
Aug 29, 2025
93df5ed
save a copy of the bam header if wanted
Aug 29, 2025
671e133
save a copy of the bam header if wanted
Aug 29, 2025
ecc1f09
save a copy of the bam header if wanted
Aug 29, 2025
1dc3931
save a copy of the bam header if wanted
Aug 29, 2025
923cbd0
fix test
Sep 16, 2025
572174e
update py-ft for new methods
Sep 16, 2025
a51ee6d
Add a ploting CLI utility for pyft just to glance at the data
Oct 22, 2025
e3b6b55
pyft versions
Oct 22, 2025
4a1f72f
pyft versions
Oct 27, 2025
f2c835c
drop merge peaks
Oct 27, 2025
7f40407
clippy
Oct 27, 2025
1aedd65
readthedocs build
Oct 27, 2025
4689c45
readthedocs build
Oct 27, 2025
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2 changes: 2 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -23,3 +23,5 @@ py-ft/test.py
py-ft/test.tbl
tests/data/shuffle.chr20.hifi.bed.gz
benchmarks/2025-07-08-new-torch-version/bin/
local-test-files/
pg-test-data/
9 changes: 7 additions & 2 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,17 @@ sphinx:
configuration: py-ft/docs/conf.py

build:
os: "ubuntu-20.04"
os: "ubuntu-22.04"
apt_packages:
- cmake
tools:
python: "3.10"
rust: "latest"
jobs:
pre_install:
# Install Rust via rustup to get a recent version
- curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable
- . $HOME/.cargo/env
- rustc --version

python:
install:
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