Hi all, So I finally got round to submit my patches for MUMmer. One can be found in the repo, half of the other is attached to this mail. Unfortunately, the other half got lost in a code reindentation. Applying the changes requires refactoring src/tigr/sw_align.cc for the changes in the header. If someone has a lot of spare time on the weekend, feel free to go ahead. Best, Fabian
81,102d80
<
< /*
< MUMmer defines a node as follows:
<
< Struct Node {
< Score S[3];
< Score *max;
< }
<
< That is a huge waste of memory. Each Score structure has seven bytes of padding
< as its end. Thus, roughly a third of the memory occupied by a node is waste.
< Using the format below values are tightly packed, making a node smaller. For a
< random, unrepresentable data the following measurements were taken:
<
< cmd: =time -f "%e %M %P" ~/bin/mugsy/MUMmer3.20/postnuc -b 200 ../../../AE.fasta ../../../BA.fasta out < ../../out.mgaps
< old: 7.51 97928 99%
< new: 6.42 63752 99%
<
< By this simple change, the used memory went down by a third and and the code
< became faster (propably due to better caching).
<
< */
105,107c83,84
< long int values[3];
< char used[3];
< unsigned char maxi;
---
> Score S[3];
> Score * max;
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