simplification of the core.py #1
Open
avvaruakshay wants to merge 20 commits into
Open
Conversation
Collaborator
|
Read the changes and i have added bitwise flags comments in core.py |
| reads_sampled +=1 | ||
| cigar = read.cigarstring | ||
| # ?? I think the read length and also if the data is SRS or LRS should be provided by the user | ||
| # ?? Also should read_length be summed? |
Collaborator
There was a problem hiding this comment.
I summed it to see the average length of the reads. Should i take a median instead
| mini_cooper(parameters, each_bam, contig, tidx, karyotype_list[kidx]) | ||
| else: | ||
| cooper(each_bam, args.regions, args.fasta, aln_format, fetcher[0], args.map_qual, out_file, seq_platform, args.snp_qual, args.snp_count, args.snp_dist, args.max_reads, args.min_reads, args.snp_read, args.phasing_read, -1, args.flank, args.debug_mode, karyotype_list[kidx]) | ||
| cooper(parameters) # ?? what is purpose of this? |
Collaborator
There was a problem hiding this comment.
For single-thread mode, this part will be executed based on SRS/LRS, but calling cooper comes only one time
|
|
||
| srs = False | ||
| if args.amplicon: | ||
| srs = True # Why is SRS true if amplicon mode is selected? |
Collaborator
There was a problem hiding this comment.
Amplicon mode - process the bam in loci-wise manner
srs with True value will call the mini_cooper / loci-wise mode
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
I have changed the
argsvariable toparameters. Passed this object as input to thecooperandmini_cooperfunctions instead of individual arguments.I added comments
# ??wherever the code is unclear or something we need to handle. Please review the code.