- UPLOADED AS v1.3.0.dev1 TO PYPI
- Fix a bug that broke iRep when skipping mm
- Translate .fasta files into all uppercase on loading them
- Removed some of the uninteresting columns from the genome_info output
- Change name of argument "filter_cutoff" to "min_read_ani"
- Add database_mode
[1.3.0q] - 2020-06-15
- Fix a bug in GW having to do with the new mapping_info
[1.3.0p] - 2020-06-11
- Add a little bit more checkpoints
- Fix the "min_genome_coverage" thing; there were problems with the read report when a scaffold had 0 reads
[1.3.0o] - 2020-06-10
- Modify how split profiling is done and modify Rdic. Now only the reads for each scaffold are passed to worker threads, through the queue. This should lead to increased run-times (though hopefully not too bad; it should only impact efficiency) and significantly decreased memory usage
- Remove "--scaffold_level_mapping_info" and have it always on
- Change how read filtering is done after mutli-processing to improve speed
[1.3.0n] - 2020-06-08
- Deep copy when making the final Rdic object in filter_reads
[1.3.0m] - 2020-06-05
- Add logging for spawning and terminating workers to check the impact on RAM
- No more global scaff2sequence; just send over with commands
- Explicitly call the garbage collector in profile
[1.3.0l] - 2020-06-04
- Add more checkpoints to filter_reads
- Adjust "ReadGroupSize" to 5000
- iRep is only run on mm = 1
- re-write \_iRep_filter_windows
- change the null_model to a regular dictionary; if a coverage isn't in there, use null_model[-1] for the biggest coverage
- change profile to no longer use globals; spawn new processes instead of forking
[1.3.0k] - 2020-06-04
- Add a sanity check to "prepare_bam_fie" for proper indexing
- Dont have get_paired_reads write to the log when multiprocessing
- Remove \_validate_splits (it takes too long)
- Add a checkpoint for loading the .fasta file
- Change filter_reads to the "spawn" rather than "fork" multiprocessing
- Change the way bam files are initilized in filter_reads
[1.3.0j] - 2020-06-02
- Make a argparse group for mm_level; calc GW on the mm level
- Plots work again
- Delete a pbar update that was crashing gene profiling in single thread mode (I think?)
- Fix partial gene identification problem
- If .sorted.bam in the name of the .bam file, dont try and sort it
- There can only be a maximum of 1000 jobs when filtering reads; hopefully cuts way down on queue access
[1.3.0i] - 2020-06-01
- Fix bug with small scaffolds and add test to catch it
- Change --min_fasta_reads to --min_scaffold_reads
- Add --min_genome_coverage to profile, along with tests to make sure it works
- Handle iRepErro and StbErrors now
[1.3.0h] - 2020-05-22
- Add some logging to gene profile in single thread mode
- Add the ability to catch iRep failures
[1.3.0g] - 2020-05-21
- Add a 5 second timeout for single thread runs
- Store fasta_loc during profile
- Store scaffold 2 length from profile, not from within the profiled splits
- iRep can now be calculated
- Replace _mm_counts_to_counts_shrunk_ with a version that preserves base order
- Add "object_type" to IS profile objects
- If interrupted during profile, kill all processes
- Output tables are all made using the "generate" command of SNVprofile
- Big changes to the actual output tables
- This version breaks lots of plots and the "compare" function! Watch out!
[1.3.0f] - 2020-05-13
- dN/dS for genes
[1.3.0e] - 2020-05-13
- Re-write of genes profiling section
- Suppress warnings made during plotting
- Add real logging report to profile_genes
- Add failure testing to profile_genes
[1.3.0d] - 2020-05-08
- Updating failure report to be better (including testing for split profiling and merging failures)
- Updating plots to not make all those errors
- Removed "MM" from all figures, replace with ANI level
- Rdic is stored by default
[1.3.0a-c] - 2020-05-08
- Paralellization of individual scaffolds is done now using windows
- This required various performance tweaks to get right