Changes

= Karma Performance Tuning =

= Karma Performance Tuning =

There are four components to the Karma index and hash.  A pure index, based on an N-mer word index.  This is used as a pointer into a word positions table, which is an ordered list of genome positions in which that N-mer word appears.  There is a cap called the ''occurrence cutoff'', which once crossed, causes that index word to be marked as a high repeat pattern.  Once marked as high repeat, the N-mer word is now combined with both the N-mer word preceding it, as well as the N-mer word succeeding it to create a 2 * N-mer word hash key.  Two hash tables are populated, a left and a right hash.

There are four components to the Karma index and hash.  A pure index array, based on an N-mer word index.  This is used as a pointer into a word positions table, which is an ordered list of genome positions in which that N-mer word appears.  There is a cap called the ''occurrence cutoff'', which once exceeded, causes that index word to be marked as a high repeat pattern.  Once marked as high repeat, the N-mer word is instead combined with both the N-mer word preceding it, as well as the N-mer word succeeding it to create a 2 * N-mer word hash key.  Two hash tables are populated, a left and a right hash.  These are then used when that pattern is found in a read.

== Index Word Size ==

== Index Word Size ==