sid-krish rhometa issues

sid-krish / rhometa

metagenome population recombination rate estimation pipeline

MIT License

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The use of subprocess.Popen in pairwise_table_paired_end.py and pairwise_table_single_end.py could be an issue

#62 sid-krish opened 3 months ago
0
Replace use of samtools pileup?

#61 sid-krish opened 8 months ago
0
Subsample fraction output needs header row

#60 sid-krish opened 8 months ago
0
Number of variants in theta_est.py in calculated incorrectly

#58 sid-krish closed 1 year ago
1
tps_mean/median_depth could be remaned for easier understanding

#57 sid-krish closed 8 months ago
0
No value keeping old code within version control.

#56 cerebis opened 1 year ago
0
Exception in `main_weighted.py` when no results returned

#55 cerebis opened 2 years ago
0
Estimating recombination rates between two populations

#54 fpusan closed 1 year ago
1
Error executing process > 'THETA_ESTIMATE (1)'

#53 azk001 closed 1 year ago
5
Larger lookup tables run out of memory with present Nextflow definition

#52 cerebis closed 1 year ago
0
Reccommend renaming some files in documentation and improve clarity

#51 cerebis opened 2 years ago
0
Error running `theat_est.nf` workflow with multi-sequence reference.

#50 cerebis closed 2 years ago
1
Error executing process > 'FILENAME_PREFIX (1)'

#49 azk001 closed 2 years ago
6
Combining all likelihood values per depth into a large df prior to final summation will result in extensive ram use

#48 sid-krish opened 2 years ago
0
bam sort step should come first?

#47 sid-krish closed 1 year ago
0
Occasionally sub-sampling a large bam produces a 0 for rho estimate for certain seed vals

#46 sid-krish closed 2 years ago
1
Theta_est.nf is missing filter_bam step from rho_est.nf

#44 sid-krish closed 2 years ago
1
in theta_est.nf samtools sort must be applied once at start

#43 sid-krish closed 2 years ago
1
Need to provide the option where lookup tables with log-scale rho range can be generated and used

#42 sid-krish closed 1 year ago
0
Exception handling / warning for when sub-sampling removes too many reads

#41 sid-krish opened 2 years ago
1
Mismatching single-end setting and bam file will cause errors

#40 sid-krish opened 2 years ago
0
Implement exception handling for converting between log-likelihood to likelihood and vice versa

#39 sid-krish opened 2 years ago
0
Output a file with runtime parameters

#38 sid-krish opened 2 years ago
0
Can the alternate allele count in the freebayes vcf be used to skip the bi-allelic filter step?

#37 sid-krish closed 2 years ago
1
Pair parsing

#36 sid-krish closed 2 years ago
0
Hdf5

#35 sid-krish closed 2 years ago
0
Have per process conda and docker config?

#34 sid-krish closed 2 years ago
1
Expression for "rho range" is counter-intuitive.

#33 cerebis opened 2 years ago
0
In the pair_parsing branch a pairwise table script for single end reads needs to be implemented

#32 sid-krish closed 2 years ago
1
number of bootstraps is not being propagated through accurately in pair_parsing branch

#31 sid-krish closed 2 years ago
1
In pair_parsing brach, if sufficient ram is not available, the program will crash under various memory related errors

#30 sid-krish opened 2 years ago
1
Example implementation of HDF5

#29 cerebis closed 2 years ago
0
Consolidate all downsampled lookup tables into a single store.

#28 cerebis opened 2 years ago
0
Version pinning needs to exclude Numpy updates above 1.21.x

#27 cerebis closed 2 years ago
4
Pair parsing

#26 sid-krish closed 2 years ago
0
`mprr_main_parallel_seeded.py` simpler "pandas-ic" calculation of rho at max likelihood.

#25 cerebis closed 2 years ago
1
`mprr_main_parallel_seeded.py` complains of deprecated `pandas.append()`

#24 cerebis closed 2 years ago
1
`gen_pairwise_table.py` scales poorly for larger real problems.

#23 cerebis closed 2 years ago
0
`gen_pairwise_table.py` does not check for BAM sort order

#22 cerebis closed 2 years ago
0
`gen_pairwise_table.py` with multiple references produces erroneous results

#21 cerebis closed 2 years ago
0
`recom_est.nf` should probably be renamed `rho_est.nf`

#20 cerebis closed 2 years ago
1
rho_meta might need to take on some responsibility to filter input BAM files.

#19 cerebis closed 2 years ago
0
recomb_est.nf could determine ldpop rho range itself

#18 cerebis opened 2 years ago
0
Making better use of Nextflow checkpointing.

#17 cerebis closed 2 years ago
0
`gen_pairwise_table.py` is *really* memory hungry.

#16 cerebis closed 2 years ago
1
process SUBSAMPLE_BAM does not use multiple cpus

#15 cerebis closed 2 years ago
0
`recomb_est.nf` does not validate command-line options.

#14 cerebis opened 2 years ago
3
Workflow parallelism (and other resources) should be user accessible.

#13 cerebis opened 2 years ago
0
Error with user option makes `recomb_est.nf` unrunnable

#12 cerebis closed 2 years ago
0
`lookup_table_gen.nf` contradictory and out of date defaults

#11 cerebis closed 2 years ago
1