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Add bam support for counting intervals #40

Merged
merged 96 commits into from
Dec 3, 2024
Merged

Add bam support for counting intervals #40

merged 96 commits into from
Dec 3, 2024

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donaldcampbelljr
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This pull request shows code that uses noodles and bigTools crates to read .bam files and export the counts to:

  • wig
  • npy
  • bedGraph
  • bw (via an intermediate bedGraph conversion)

Addresses #30

@donaldcampbelljr donaldcampbelljr changed the title Add bam -> bw, bed support Add bam support for counting intervals Oct 24, 2024
@donaldcampbelljr donaldcampbelljr changed the base branch from master to dev October 24, 2024 15:58
@donaldcampbelljr donaldcampbelljr mentioned this pull request Oct 24, 2024
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8 tasks
@donaldcampbelljr
add attempt at determining Map length (commented out)
ef19243
@donaldcampbelljr
add bedGraph count compression
c7cb01b
@donaldcampbelljr
finish adding bedGraph count compression
80bf9c5
@donaldcampbelljr
fix mutability issue for bam reading into chrom vec
65e1a62
@donaldcampbelljr
change sorted to start instead of all for BedGraphToBigWigArgs
a0dfb75
@donaldcampbelljr
Merge pull request #41 from databio/dev_bedGraph_compress_counts
2410c30 
Dev bed graph compress counts
@donaldcampbelljr
Add bam and bai examples, cargo fmt
32f3072
@donaldcampbelljr
begin refactoring to have bam processing be its own workflow
b0dc3a4
@donaldcampbelljr
refactor get_final_chromosomes to uniwig utils
de8be6d
@donaldcampbelljr
add future instructions
034fe51
@donaldcampbelljr
add narrowpeak test
a944da1
@donaldcampbelljr
Merge remote-tracking branch 'origin/dev_bam_bedgraph_bigtools' into …
fb5dccc 
…dev_bam_rewrite
@donaldcampbelljr
change test back to using temp dir
36c2abb
@donaldcampbelljr
add parallel reading of header from bam file
2fe8c81
@donaldcampbelljr
add out selection enum, begin adding match statements before counting
ac1acc1
@donaldcampbelljr
refactor to pass iterator to couting func for bam counting
a67409e
@donaldcampbelljr
set up file for specific file output types immediately upon beginning…
eb8f057 
… count
@donaldcampbelljr
some refactor to use new header/reader for each match of start end core
08d6922
@donaldcampbelljr
return a boxed file OR std_out
64cc3fc
@donaldcampbelljr
cargo fmt
5102119
@donaldcampbelljr
attempt to set up bedgraph streaming via stdin to bigtools (does not …
7bf1df2 
…work yet)
@donaldcampbelljr
attempt using outb: BigWigWrite<File>
1da7d0d
@donaldcampbelljr
Revert "attempt using outb: BigWigWrite<File>"
158912d 
This reverts commit 1da7d0d.
@donaldcampbelljr
rethink approach, some errors still need to be resolved
ea4b141
@donaldcampbelljr
more work towards fixed_start_end_counts_bam_to_bw
ab4af2b
@donaldcampbelljr
fix compile errors
cc87462
@donaldcampbelljr
edit error messages to aid in debug
3d16aee
@donaldcampbelljr
add checking for first record to earlier in process of bam, rethink s…
cd51417 
…ome messaging
@donaldcampbelljr
add debug argument for more verbose messaging for non-existent chroms…
4763a60 
… and records
@donaldcampbelljr
add cleaning up bigwig files AFTER merge
c41dbfa
@donaldcampbelljr
add output_bam_counts_non_bw
d8de2d1
@donaldcampbelljr
remove zoom args for now
8679df6
@donaldcampbelljr
change interval to use prev_count
a75c766
@donaldcampbelljr
begin refactor to support bed file as bam output
12610f3
@donaldcampbelljr
add bam_to_bed_no_counts and process_bed_in_threads
e22794c
@donaldcampbelljr
add combining final bed files
e0d6f5c
@donaldcampbelljr
fix tests by adding debug bool
6c2a538
@donaldcampbelljr
add assessing flags via bit operations
a9ee5a5
@donaldcampbelljr
some clean up
2b893de
@donaldcampbelljr
more clean up
6914ad7
@donaldcampbelljr
more more clean up
14c6c3d
@donaldcampbelljr
more more more clean up
02aaf86
@donaldcampbelljr
last warnings cleaned
2c6763d
@donaldcampbelljr
cargo fmt
2fe6a09
@donaldcampbelljr
add counttype argument. Only works for bam processing
9227974
@donaldcampbelljr
fix tests
ad0e96f
@donaldcampbelljr
format
cc21a18
@donaldcampbelljr
update docs
86352d7
@donaldcampbelljr
update readme
211e2d3
@donaldcampbelljr
Merge pull request #47 from databio/dev_bam_rewrite
aa719c5 
Refactor bam to bw workflow
@donaldcampbelljr donaldcampbelljr marked this pull request as ready for review December 3, 2024 16:43
@donaldcampbelljr
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Going ahead with merge since the majority of code review was in the previous PR #47

@donaldcampbelljr donaldcampbelljr merged commit 60b6b4b into dev Dec 3, 2024
@donaldcampbelljr donaldcampbelljr deleted the dev_bam_bedgraph_bigtools branch December 3, 2024 16:50
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@donaldcampbelljr