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Low Activity
Commits
: Listings
Analyzed
1 day
ago. based on code collected
1 day
ago.
Jul 22, 2024 — Jul 22, 2025
Showing page 47 of 351
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Partition kmer evidence into 100 Mbp chunks, then let meryl pick how many chunks to process at once.
Brian P. Walenz
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almost 7 years ago
Remove non-functional haplotype support from submitScript().
Brian P. Walenz
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almost 7 years ago
Adjust memory usage estimate. It's still under-reporting memory used though.
Brian P. Walenz
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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.
Brian P. Walenz
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almost 7 years ago
Explicitly initialize bestPrefix in findBestPrefixSize().
Brian P. Walenz
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almost 7 years ago
Update estimates of amount of sequence in compressed files, though it's probably off by 2 for FASTQ.
Brian P. Walenz
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almost 7 years ago
Add secret option -E to estimate the number of bases that could be counted in some memory size.
Brian P. Walenz
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almost 7 years ago
Stop logging INITIALIZE during merylOperation::initialize(). I don't need a reminder that it's not doing the right thing.
Brian P. Walenz
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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.
Brian P. Walenz
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almost 7 years ago
Fix issue with older perl and two adjacent code labels.
Brian P. Walenz
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almost 7 years ago
Skip FASTQ QV line using 'next', not 'continue'.
Brian P. Walenz
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almost 7 years ago
Fix error in error message.
Brian P. Walenz
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almost 7 years ago
Remove the original 'project kmer' meryl and associated libraries. Roughly 14.5 years old in its current form.
Brian P. Walenz
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almost 7 years ago
Add support for trio-binning to canu.
Brian P. Walenz
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almost 7 years ago
Fix minor memory leak; minor cleanup.
Brian P. Walenz
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almost 7 years ago
Update comment to reflect reality.
Brian P. Walenz
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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.
Brett T. Hannigan
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almost 7 years ago
Update kmerCountExactLookup test code to handle dropping low/high frequency kmers.
Brian P. Walenz
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almost 7 years ago
Fix kmerCountExactLookup so it can drop low/high count kmers when loading data.
Brian P. Walenz
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almost 7 years ago
Load the statistics data upon trying to access it.
Brian P. Walenz
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almost 7 years ago
Add maxFrequency() to return the largest count in the histogram.
Brian P. Walenz
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almost 7 years ago
Merge pull request #1082 from rick-heig/patch-2
Sergey Koren
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almost 7 years ago
* Improving error message
Brett T. Hannigan
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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.
Brett T. Hannigan
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almost 7 years ago
Process the dump inclusively too
Sergey Koren
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almost 7 years ago
Fixed typo in fast execution message
rick-heig
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almost 7 years ago
Update faq.rst
Sergey Koren
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almost 7 years ago
Don't stop after completing meryl. D'oh!
Brian P. Walenz
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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.
Brian P. Walenz
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almost 7 years ago
Add thresholding based on fraction-distinct and word-frequency.
Brian P. Walenz
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almost 7 years ago
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