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fq trimming #37

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fq trimming #37

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150c4be
WIP: fq stuff
brentp Aug 16, 2023
0957ea3
change max_diffs to max_overlap_error_rate
brentp Aug 16, 2023
73f78b8
renaming
brentp Aug 16, 2023
e2bdcfa
start of CLI stuff.
brentp Aug 17, 2023
f48a5c3
we have readers and writers
brentp Aug 17, 2023
476ebfc
reading and writing fastqs
brentp Aug 17, 2023
fe8af74
actually correct based on overlap
brentp Aug 17, 2023
9d54bec
moving average and base-quality
brentp Aug 18, 2023
884dca3
match input output names to Tim's example
brentp Aug 18, 2023
5efdf45
parsing of operations enum
brentp Aug 18, 2023
a164b37
main execution loop
brentp Aug 18, 2023
a4083b7
copy Tim's oscillation detection from python to rust
brentp Aug 21, 2023
38f077c
more efficient identify_trim_point for oscillations
brentp Aug 21, 2023
bb4a10f
prevent some underflows
brentp Aug 21, 2023
d56a65a
stub out stats
brentp Aug 22, 2023
1ea71c0
cleanup stats
brentp Aug 23, 2023
a68e6e3
try to clarify option usage.
brentp Aug 23, 2023
e21631a
more stats
brentp Aug 23, 2023
fc58ca1
bug fixes and read length stats
brentp Aug 23, 2023
5b3043e
naming and length hist update
brentp Aug 23, 2023
6201ea1
add Cargo.lock
brentp Aug 24, 2023
7a2e646
logging in pair overlap
brentp Aug 24, 2023
987d34e
warn that output files are always bgzipped
brentp Aug 29, 2023
7263c5c
fix erroneous warning about .gz extension
brentp Oct 20, 2023
c351467
clippy: PathBuf -> Path
brentp Oct 23, 2023
62258d7
fix case where there is no overhang from R1
brentp Oct 23, 2023
2ee4d93
handle no overhang in r1 with adapter in r2
brentp Oct 23, 2023
382e2a6
Io::is_gzip_path
brentp Oct 24, 2023
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,2 +1,4 @@
/target
.vscode
*.fq
*.fq.gz
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