0
I Use This!
Low Activity

Commits : Listings

Analyzed 1 day ago. based on code collected 1 day ago.
Jul 22, 2024 — Jul 22, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Partition kmer evidence into 100 Mbp chunks, then let meryl pick how many chunks to process at once. More... almost 7 years ago
Remove non-functional haplotype support from submitScript(). More... almost 7 years ago
Adjust memory usage estimate. It's still under-reporting memory used though. More... almost 7 years ago
Allocate merylCountArray as an array, not an array of pointers. Change how memory is accounted for to solve severe performance degradation with large prefixes. More... almost 7 years ago
Explicitly initialize bestPrefix in findBestPrefixSize(). More... almost 7 years ago
Update estimates of amount of sequence in compressed files, though it's probably off by 2 for FASTQ. More... almost 7 years ago
Add secret option -E to estimate the number of bases that could be counted in some memory size. More... almost 7 years ago
Stop logging INITIALIZE during merylOperation::initialize(). I don't need a reminder that it's not doing the right thing. More... almost 7 years ago
Don't try to find/estimate uncompressed size of gz/bz2 files in AS_UTL_sizeOfFile(); gzip can't report sizes larger than 2GB and bzip2 was just a bad guess. More... almost 7 years ago
Fix issue with older perl and two adjacent code labels. More... almost 7 years ago
Skip FASTQ QV line using 'next', not 'continue'. More... almost 7 years ago
Fix error in error message. More... almost 7 years ago
Remove the original 'project kmer' meryl and associated libraries. Roughly 14.5 years old in its current form. More... almost 7 years ago
Add support for trio-binning to canu. More... almost 7 years ago
Fix minor memory leak; minor cleanup. More... almost 7 years ago
Update comment to reflect reality. More... almost 7 years ago
Updating stash to DNAnexus cloud * Switching from dx upload to ua to allow for resuming an upload * For the cases where the upload is streaming from stdin, we still need to worry about removing any incomplete files as uploading from stdin is not resumable. More... almost 7 years ago
Update kmerCountExactLookup test code to handle dropping low/high frequency kmers. More... almost 7 years ago
Fix kmerCountExactLookup so it can drop low/high count kmers when loading data. More... almost 7 years ago
Load the statistics data upon trying to access it. More... almost 7 years ago
Add maxFrequency() to return the largest count in the histogram. More... almost 7 years ago
Merge pull request #1082 from rick-heig/patch-2 More... almost 7 years ago
* Improving error message More... almost 7 years ago
Updating stash code to retry on an upload failure when stashing to DNAnexus * Currently when stashing files to the DNAnexus platform the code does not check the return code to make sure the upload was successful. * This change uses a simple wrapper around dx upload to check the return code and retry up to 5 times if the upload fails. If it still is not successful, it will print out an error message. More... almost 7 years ago
Process the dump inclusively too More... almost 7 years ago
Fixed typo in fast execution message More... almost 7 years ago
Update faq.rst More... almost 7 years ago
Don't stop after completing meryl. D'oh! More... almost 7 years ago
Replace 'old meryl' with 'new meryl'. Change the way frequent kmers are computed, hopefully finally resolving issue #796. TrioCanu is currently broken. More... almost 7 years ago
Add thresholding based on fraction-distinct and word-frequency. More... almost 7 years ago