TODO

TODO for malfoy part -> index/anchoring
-replace hash table with MPHF
-opti gestion of reversecomplement
-try to index a fraction of the reference kmer to see the impact on mapping
-replace kmer counting by kmc2
-multhithreading
-exposing more parameters in command line (hamming vs ssw and maybe missrate)


TOUDOU for camille part -> mapping/alignment
-improve SSW
-add bowtie/bwa like mapping
-produce a score instead of a bool
-produce SAM output or alignement output
-adding folders

DOUDOU for Simon part -> scripting
-Produce bench and keep track of performances through the commit ?
-script blat precision and recall (see kami)
-multithreading ?



NOTES:

RESULT OF BOWTIE2 minicoli on ecoliref
Time loading reference: 00:00:00
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
Multiseed full-index search: 00:00:23
500000 reads; of these:
  500000 (100.00%) were unpaired; of these:
    13226 (2.65%) aligned 0 times
    470857 (94.17%) aligned exactly 1 time
    15917 (3.18%) aligned >1 times
97.35% overall alignment rate
Time searching: 00:00:23
Overall time: 00:00:23

Time to beat :
23s
Alignement rate to beat
97.35%