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Working on v0.5.0 #50

Merged
merged 139 commits into from
Jul 31, 2024
Merged

Working on v0.5.0 #50

merged 139 commits into from
Jul 31, 2024

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mrvollger
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@mrvollger mrvollger commented Apr 9, 2024 •
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  • feat: add the samtools filter flag -F to all commands, this is a breaking change as it makes small adjustments to the CLI
  • feat: unify the input and output bam handling
  • fix: pyft doc CI build
  • feat: Add a pileup command that gives per-base summaries of fiber-seq data.
  • fix: label on FIRE vs LINKER for decorator tracks

mrvollger added 30 commits April 9, 2024 14:25
@mrvollger
start work on making a fire track
351cb91
@mrvollger
chore: cargo dist
3ca6260
@mrvollger
fix: py-ft build
714a8dc
@mrvollger
fix: py-ft build
9c4dea1
@mrvollger
feat: inital fibertools pileup is complete
f512b19
@mrvollger
feat: inital fibertools pileup is complete
20e4ef6
@mrvollger
feat: inital fibertools pileup is complete
b4ac782
@mrvollger
clean
8b6a1ac
@mrvollger
feat: allow fire opts to be read from env vars.
3fea667
@mrvollger
chore: extend docs #54
6260d39
@mrvollger
chore: hide m5c #54
b5dfd1e
@mrvollger
chore: hide m5c #54
956474d
@mrvollger
feat: add a pyft way to iterate over a bam file one read at a time.
831e5a0
@mrvollger
chore: pyft bump
49b5e83
@mrvollger
feat: pileup is now useable
9a2530a
@mrvollger
feat: pileup is now useable
f709630
@mrvollger
feat: pileup is now useable
844f2a2
@mrvollger
chore: prep for bump
95d5ddb
@mrvollger
feat: allow the complexity of the pipeup to be adjusted
16c18ee
@mrvollger
todo: why are the revio tests failing?
c887abc
@mrvollger
fix: add new check to avoid a new failure on unaligned bams
7ec0651
@mrvollger
test a fix for doc build error
20a16d2
@mrvollger
test a fix for doc build error
4389dc5
@mrvollger
test a fix for doc build error
5714739
@mrvollger
test a fix for doc build error
112c581
@mrvollger
fix:add target names to pyft
7357ab0
@mrvollger
fix:add target names to pyft
370ea24
@mrvollger
fix:add target names to pyft
fbc50c5
@mrvollger
test a fix for doc build error
7a190a1
@mrvollger
test a fix for doc build error
15274ea
mrvollger added 18 commits July 19, 2024 22:20
@mrvollger
get ucsc tools into conda
2b9d282
@mrvollger
fix: missing final base in pileup region
bff5459
@mrvollger
feat: skip empty regions
1e75fb4
@mrvollger
feat: skip empty regions
e088980
@mrvollger
fix: check for end of chrom
69942fe
@mrvollger
fix: use min ml score in pileup
0d035ce
@mrvollger
fix: use bit flag filter
a959126
@mrvollger
refactor: Make the inputbam function a utility and add a FiberFilter …
f8f2f43 
…structure that can be used to filter the input bam and therefore the output
@mrvollger
refactor: Breakout subcommands opts into different files
1751215
@mrvollger
refactor: move the running of subcommands into a submodule called sub…
c838410 
…commands
@mrvollger
refactor: move the running of subcommands into a submodule called sub…
b3bcece 
…commands
@mrvollger
refactors: removing unneeded nesting
9a92b67
@mrvollger
refactor: move some complexity into utils
d4e3977
@mrvollger
refactor: move some complexity into utils
10c4210
@mrvollger
refactor: move some complexity into utils
6d590e3
@mrvollger
refactor: move some complexity into utils
9d54591
@mrvollger
refactor: move some complexity into utils
4796b8b
@mrvollger
refactor: update for fibertools refactor
2fa2518
@mrvollger mrvollger changed the title 0.4.3 Working on v1.0.0 Jul 24, 2024
@mrvollger mrvollger changed the title Working on v1.0.0 Working on v0.5.0 Jul 31, 2024
@mrvollger mrvollger merged commit 198cebe into main Jul 31, 2024
8 of 9 checks passed
@mrvollger mrvollger deleted the 0.4.3 branch July 31, 2024 02:53
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