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fix bug on readlen #59
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Sample-specific fragment GC bias and other changes
fixed bug wrt strand specific simulation
Matrices, son.
fix input validation for gcbias
Basemeans uninitialized in case num_reps == 1
When using 'meanmodel=T', the reads_per_transcript in simulate_experiments() might be non-positive.
bugfix - avoids duplicated read IDs
Keep reads_per_transcript positive
Thanks so much for the PR! I'd be happy to merge; have you tested the change and have you confirmed that it produces expected output? If you could paste small test cases here (or add tests) that would be amazing. Really appreciate it! |
Sure @alyssafrazee . Below is a test case using the example from the section 'Using real data to guide simulation' in your bioconductor introduction.
When specifying
This PR fixes the error, and the read lengths in the output files are also correct:
Thanks, |
Hi @alyssafrazee ,
This PR fixes the same error as #24 when specifying readlen in the function:
Error in seq_gtf(gtf, seqpath, ...) : unused argument (readlen = 70)
The error also shows up in the functions simulate_experiment_empirical and simulate_experiment_countmat.
I hope it would be helpful.
Thanks,
Renee