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7bgzf

  • a suite of DEFLATE (RFC 1951) algorithms
  • contact: please use my github profile or the email on the paper (now published!)

Building Instruction

  • 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).
      • The simplest way is to change config.mk.in @Hsource@HTSLIB = $(HTSDIR)/libhts.a to libhts.so.
      • Note: configure --enable-plugins does not work as symbols in exe are prioritized than LD_PRELOAD.
    • 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.

Side notes (oh I can write this as the paper is published)

  • 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.