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TODO
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TODO
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find-knot speedup:
- too many redundant rounds of partitioning?
memory improvement for counting hash
sequence loading into both counting & hashbits
graphsize filtering with stop-big-traversal
why does stop-big-traversal still connect???
cython integrate!
pull reads into partitions?
look more assiduously for memory leaks
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counting hash generalization to n < 8 bits => memory efficiency
load-counting/bigcount loading is slooooow
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screed slice
screed fasta/fastq output
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fix tests cleanup
pyrex/cython stuff
docs!
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the N dilemma
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put in logging.
fix tests and test cases to properly isolate/remove temp files.
fix dir(ht)
###
Semi-obsolete comments, pre partitioning:
also, can probably arrange parallelization split & hash table size so
that modulus exactly fills split portion of table.
mismatch hashing - compute min num - each base?
copyright, C++ file comments at top; license; etc.
tests for readmask updating, etc. in various circumstances!
tests for khmer saturation vs valid reads
profiling
reading on hash functions:
http://www.burtleburtle.net/bob/hash/doobs.html
http://www.burtleburtle.net/bob/c/lookup3.c
http://www.burtleburtle.net/bob/hash/doobs.html
http://www.codinghorror.com/blog/2007/12/hashtables-pigeonholes-and-birthdays.html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131890/
things to reference or at least look at:
http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Getting_Started_with_Meryl
http://www.hgsc.bcm.tmc.edu/cascade-tech-software_bang-ti.hgsc
http://www.hgsc.bcm.tmc.edu/cascade-tech-software_cbt-ti.hgsc
http://code.google.com/p/google-sparsehash/