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cancerit / cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis
http://cancerit.github.io/cgpCaVEManWrapper/
GNU Affero General Public License v3.0
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WIP: Hotfix/1.17.1 #56

Closed keiranmraine closed 3 years ago

keiranmraine commented 3 years ago

For sanity check only

Trivial review, using libdeflate compiled htslib for caveman requires only updating the base container:

ubuntu@6d64a17d4fa8:~$ ldd $(which caveman)
...
    libdeflate.so.0 => /opt/wtsi-cgp/lib/libdeflate.so.0 (0x00007fed20947000)
...

Internal CI shows following CPU time differences:

Data type 1.17.0 (s) 1.17.1 (s) diff (s) % of original
Amplicon 3272 3043 -229 93.00%
Targeted 13911 13777 -134 99.04%
WXS 145279 118187 -27092 81.35%
WGS 2186185 2122906 -63279 97.11%

Improvement is using formular new/old*100%, where the result shows the percentage of the original time it now takes.

davidrajones commented 3 years ago

Are there no changes required for CaVEMan core w.r.t. libdeflate that need to go into this?

keiranmraine commented 3 years ago

@davidrajones no, as shown above the caveman binary is linking libdeflate as htslib is using it under the hood.

You may want to add something to the CaVEMan install/wiki about compiling htslib with libdeflate.