[khmer] Counting kmers and disabling reverse complement

[C. Titus Brown]

On Sun, Jun 16, 2013 at 01:09:18AM -0700, Lester Mackey wrote:
> Hi Jordan,
> 
> If, after running 'make clean' in all directories, I set NO_UNIQUE_RC=1 in
> 'lib/Makefile' and then run 'make' in the higher level python directory,
> the Makefile fails to add -dNO_UNIQUE_RC=1 to CXXFLAGS when compiling the
> code in 'lib' (and so the reverse complement and kmer are still treated
> identically).
> 
> I've gotten around this by adding -dNO_UNIQUE_RC=1 to CXXFLAGS explicitly
> in python/Makefile, but I wanted to let you know in case this was not the
> desired behavior.

Thanks, Lester.  I'll file this as a bug report.

--titus

> On Fri, Jun 14, 2013 at 5:53 AM, Jordan Fish <jrdn.fish at gmail.com> wrote:
> 
> > Hi Lester,
> >
> > Unless you are working with fairly small k-values you will probably want
> > to use the CountingHash.  Ktable handles simple exact counting so far
> > large-ish values of k (>12, according to
> > http://khmer.readthedocs.org/en/latest/ktable.html) it'll blow up.
> >
> > The counting hash uses a bloom filter to limit memory usage at the cost of
> > in-exact counting.  Hopefully titus will jump in here with a link to some
> > documentation on the inexact counting.
> >
> > Finally, if you want to force khmer to treat a kmer and it's reverse
> > complement as unique you will need to edit 'lib/Makefile' and change the
> > line
> >
> > NO_UNIQUE_RC=0
> >
> > to
> >
> > NO_UNIQUE_RC=1
> >
> > and rebuild khmer
> >
> > Jordan
> >
> > On Fri, Jun 14, 2013 at 3:22 AM, Lester Mackey <lmackey at stanford.edu>wrote:
> >
> >> Dear khmer Discussion List,
> >>
> >> If my goal is to obtain a vector of kmer counts quickly from a FASTA or
> >> FASTQ file, is there any reason to prefer ktable to one of your other data
> >> structures, like the counting hash table?
> >>
> >
> >> I've noticed that ktable hashes a kmer and its reverse complement to the
> >> same bin.  Is there an easy way to disable this feature (and thereby count
> >> each kmer and reverse complement separately)?
> >>
> >> Thanks,
> >> Lester
> >>
> >> _______________________________________________
> >> khmer mailing list
> >> khmer at lists.idyll.org
> >> http://lists.idyll.org/listinfo/khmer
> >>
> >>
> >

> _______________________________________________
> khmer mailing list
> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer


-- 
C. Titus Brown, ctb at msu.edu