Informatics Research k-mer Tools Activity
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Activity for Informatics Research k-mer Tools
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Liubov Chuprikova modified a comment on ticket #33
No. My goal was to provide some tests for Continuous Integration System inside Debian. But according to Debian Statistics there are some active users of ATAC and other binaries inside k-mer tools [1]. It would be great if you prepare a new versioned release of ATAC for downloading. Thank you! [1] https://qa.debian.org/popcon.php?package=kmer
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No, my goal was to provide some tests for Continuous Integration System inside Debian. But according to Debian Statistics there are some active users of ATAC and other binaries inside k-mer tools [1]. It would be great if you prepare a new versioned release of ATAC for downloading. Thank you! [1] https://qa.debian.org/popcon.php?package=kmer
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Dan Bolser posted a comment on ticket #33
Thanks for looking at this Liubov. Are you actively using ATAC?
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fix wrong evaluation order of an expression
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Informatics Research k-mer Tools released /meryl-r2013.tar.xz
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matchExtender: Assertion `0' failed
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Brian Walenz committed [r2013]
Big rewrite of interface. Much simpler to use....
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Remove bzip2 libraries from linking. They're n...
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Afif Elghraoui created ticket #3
manpages for the meryl package
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Wow, thanks for the example! The crash was caused by the query having zero mers in...
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Possible mapMers bug with "-stats" option
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Use zero-count mers when computing -stats.
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Don't divide mean by zero.
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Marc Hoeppner posted a comment on ticket #31
I should add that I use r209 (downloaded last week)
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Possible mapMers bug with "-stats" option
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Add tar, remove subversion.
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Notes on what files to remove for the various p...
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Add 'unlink' and 'nomasking' options.
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Fix load balancing when -memory and -threads ar...
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Increase length of matches from 10k to 1m.
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Clean up meryl/libkmer installation. Add READM...
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Update, ESTmapper and ATAC are now installed in...
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Add README.atac.
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Revision 2001 fixes this issue by rewriting the input fasta files instead of symlinking...
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KeyError in DNA.DNA.reversecomplement()
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Rewrite input fasta files to resolve 'KeyError ...
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For positions with no kmer coverage, set the mi...
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Use the configured gcc/g++ for dependency gener...
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Correctly handle missing mers.
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Just a basic rewrite.
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Minor; typo in comment.
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Initialize the random access flag.
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A mere 18Tb free on that device, so I don't think that's the issue. Unfortunately,...
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Possible. I'll check.
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Uh?
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The error message is indicating the name of the file isn't set. The filenames are...
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The partitionmap output....wow, that's quite obnoxious. With values as-text, and...
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I'm guessing this was an issue back 2008 when 16gb was "LOTS of memory". 'seagen'...
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From memory (my memory, not the computer), it's reporting matches between the unique...
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What's weird is that I've seen the -crossspecies mode run in other cases.
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What does seatac do?
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Is this still an issue? Can you explain the output of leaff --partitionmap and how...
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Error running ATAC in --crossspecies mode
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Putting the sequence 'all on one line' in the input fasta fixed the issue we were...
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Yeah, the 1-to-1 requirement is 'breaking' some of our alignments, so I'm trying...
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I've been fortunate in avoiding that type of analysis directly. ;-) We've used nucmer...
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Ah, I remember this now. I thought the pipeline did this itself, but obviously not....
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The formatting is messed up by the #'s at the start of the line. :-( I think this...
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KeyError in DNA.DNA.reversecomplement()
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Sorry, can't seem to edit to fix formatting...
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KeyError in DNA.DNA.reversecomplement()
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Thanks Brian, by space-based, do you mean zero offset? We aren't seeing this uniquely...
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-L should filter kmers with count below some threshold; -H similar. -M max (or min)...
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Tagged 'ESTmapper'. Inside there, no idea. The last step, iirc, is to generate statistics...
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I will guess this is a reverse complement base-based vs space-based problem. I won't...
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Closed.
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caught std::bad_alloc in seatac step
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Given it's almost six years old, I'm not even sure it still applies.
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From which tool?
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What should they do?
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Can you add more details here?
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Did this patch get merged?
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Can you submit a patch to fix this?
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Can I close this now?
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Alignments sometimes off by one?
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Rename ESTmapper documentation.
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Rename 'mask.C' to 'kmer-mask.C'.
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Disable glibc parallel sorting; we aren't big e...
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Initialize intervalList (depth mode). Compiler...
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Add a 'value' to the interval list, and rename ...
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Rename defined constant to avoid name conflict.
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...and fix the Makefile to remove the now delet...
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Template-ify the intervalList.
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More max() to MAX() conversion.
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Replace min() and max() with MIN() and MAX() to...
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Update command line usage.
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Preserve mate pairing, by classifying mates wit...
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Multithread.
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Interface changes; filter output based on amoun...
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Accept sim4db, nucmer coords and the original e...
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Fix invert() to handle cases with one interval.
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Update alignment scores before removing alignme...
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Remove logging and make logging obey 'verbose' ...
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Better support for stdin, and gzip, bzip2 and x...
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Ignore a failed seek() on creation, for when th...
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Significant update. Masks kmers from sequences.
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Dead code.
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Fix dependencies when Python.h isn't in the sta...
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Install renamed uint32List.H.
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Replace u32bit (etc) types with more standard u...
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