fedarko strainFlye issues

fedarko / strainFlye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes

BSD 3-Clause "New" or "Revised" License

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issues

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Add option to disable partially-mapped reads filter on align command

#71 fedarko opened 1 month ago
0
Bizarre mamba installation error for a python 3.7.16 environment

#70 fedarko opened 1 year ago
1
Speed up (using mamba) and fix the CI; better installation documentation

#69 fedarko closed 1 year ago
1
CI breaks when installing skbio

#68 fedarko closed 1 year ago
0
Fix build (add lower pin for pysam)

#67 fedarko closed 1 year ago
1
Build (pysam installation) is breaking?

#66 fedarko closed 1 year ago
2
Reject contigs with names that would break bcftools

#65 fedarko opened 1 year ago
0
Use pyfaidx to access contigs in FASTA files

#64 fedarko opened 2 years ago
0
Output un-normalized coverages from "dynam covskew"

#63 fedarko opened 2 years ago
0
More efficient contig subsetting

#62 fedarko opened 2 years ago
0
Fix CI warnings from GitHub Actions

#61 fedarko opened 2 years ago
0
Consistent behavior on delaying creation of the output file(s) / output directory

#60 fedarko opened 2 years ago
0
Close BAM files after every command / test that loads them

#59 fedarko opened 2 years ago
0
Combining downstream commands

#58 fedarko opened 2 years ago
0
Ensure that contig names can be used within filenames

#57 fedarko opened 2 years ago
0
pipeline PNG might be too high quality

#56 fedarko closed 1 year ago
2
Allow --min-read-number (p-mutation calling) to be a float

#55 fedarko closed 2 years ago
0
Including (some) rare mutations from the decoy contig in the "fdr fix" BCF?

#54 fedarko opened 2 years ago
0
Compress TSV outputs?

#53 fedarko opened 2 years ago
0
Fix FDR curve plotting notebook

#52 fedarko closed 2 years ago
1
Replace lists of numbers used for diversity index p / r values with multiple=True?

#51 fedarko opened 2 years ago
0
Mamba installation instructions and CI

#50 fedarko closed 1 year ago
0
Use an approximation for the coldspot gap p-value computation

#49 fedarko closed 2 years ago
0
Output file of "unreasonable position" information during naive calling

#48 fedarko opened 2 years ago
0
Add "all" option for decoy contexts

#47 fedarko closed 2 years ago
0
Remove info flag to BCF files for "unreasonable" positions :|

#46 fedarko closed 2 years ago
0
Refactor FDR estimation command to support handling multiple decoy contexts at once; port over CP2 decoy

#45 fedarko closed 2 years ago
0
Smoothed read creation: only (re-)compute average coverages for contigs with > 0 mutations

#44 fedarko opened 2 years ago
0
Speed up input BCF validation

#43 fedarko opened 2 years ago
0
Modify hotspot command to ignore features on non-BCF contigs?

#42 fedarko closed 2 years ago
0
Allow user to (optionally) pass diversity indices to smooth create, to provide average coverages

#41 fedarko closed 2 years ago
1
BCF tempfile test race condition

#40 fedarko closed 2 years ago
1
Parameter strings

#39 fedarko closed 2 years ago
0
Make the BCF tests delete temporary *.bcf and *.bcf.csi files after running

#38 fedarko closed 2 years ago
1
Warn / fail when we encounter massive datasets?

#37 fedarko opened 2 years ago
0
Parallelizing certain operations

#36 fedarko opened 2 years ago
0
Warn user if an input BCF contains no mutations across any contigs

#35 fedarko opened 2 years ago
0
Notes on overwriting

#34 fedarko opened 2 years ago
0
Extra sanity checking: when multiple inputs are given, check that contig lengths match?

#33 fedarko closed 2 years ago
1
Notes on running commands on only certain contigs

#32 fedarko closed 2 years ago
0
Support circular GFF3 features in hotspot detection?

#31 fedarko opened 2 years ago
0
Sort out whether or not we support arbitrary BCF files for downstream steps

#30 fedarko closed 2 years ago
2
Additional minimap2 parameters that are useful for HiFi data

#29 fedarko opened 2 years ago
0
Generalize to multi-allelic mutations

#28 fedarko opened 2 years ago
0
Clearer explanation of "rare" / indisputable mutations in the tutorial?

#27 fedarko opened 2 years ago
0
Document automatic decoy contig selection somewhere

#26 fedarko closed 2 years ago
0
Make the naive calling methods output (indexed) BCF, instead of VCF

#25 fedarko closed 2 years ago
0
Add contig header to call output

#24 fedarko closed 2 years ago
0
Switch minimap2 alignment preset based on installed version?

#23 fedarko closed 2 years ago
0
Throw error in align if less than two contigs are present

#22 fedarko closed 2 years ago
0