- a suite of DEFLATE (RFC 1951) algorithms
- contact: please use my github profile or the email on the paper (now published!)
-
Execute compile.sh.
- 7bgzf is almost static; the dependency is only libc.
-
p7zip and htslib could be installed by system administration command.
-
7bgzf.so can be injected into libhts.so using LD_PRELOAD environment variable.
- However, since LD_PRELOAD utilizes procedure linkage table (PLT), samtools / bcftools need to link to libhts.so (not a).
- BGZF_METHOD environment variable is used to set the compression method. For example, BGZF_METHOD=libdeflate12 means libdeflate level 12.
- Example:
BGZF_METHOD=libdeflate12 LD_PRELOAD=./7bgzf.so samtools view ...
-
Detailed instruction for my ARM assessment should be available on the paper supplementary data.
- on-the-fly conversion of compressed files
I have not mentioned explicitly in the paper, but that conversion means PetaGene. They say they provide virtual filesystem via LD_PRELOAD. But I was not able to get evaluation copy - they say no personal evaluation.