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Branch: master
Commits on Apr 22, 2019
Commits on Jun 13, 2018
Commits on Jun 12, 2018
  1. fixes prev fix for esl_alloc_benchmark compiler warning

    cryptogenomicon committed Jun 12, 2018
    The previous fix wasn't sufficient, but this one is.
Commits on Jun 11, 2018
Commits on Jun 9, 2018
  1. Fixes for HMMER #141 and #120: compile fails on i586, ppc64be.

    cryptogenomicon committed Jun 9, 2018
    Keep PTHREADS_CFLAGS separate from CFLAGS, so user can override CFLAGS
    without messing with autoconf of pthreads.
    
    Updates version to 0.45-dev.
Commits on Jun 7, 2018
Commits on Jun 6, 2018
  1. Adds detection and support for "SSE4" vs. "SSE" vector implementations.

    cryptogenomicon committed Jun 6, 2018
    In ef206c4, I made our "SSE" vector implementation depend on <=SSE4.1
    instead of <=SSE2. I was rewriting the H4 SSV filter to use the signed
    8-bit ints and a esl_sse_hmax_epi8() macro that uses the SSE4.1
    _mm_max_epi8() intrinsic. Presciently, I noted that if this change
    were going to cause trouble, it would be on AMD platforms;
    incorrectly, I proposed that since AMD processors have supported
    SSE4.1 since AMD Bulldozer (2011), I didn't expect trouble. Well,
    trouble: Odyssey head nodes are AMD Phenom II X4 910e processors,
    circa January 2010. I hadn't noticed a problem before because I've
    been using eddyfs01 as my head node, which has Intel processors.
    
    This commit separates detection and support for "SSE" versus "SSE4"
    vector implementations. SSE requires <=SSE2 (HMMER3); SSE4 requires
    <=SSE4.1 (current HMMER4).
    
    This commit will temporarily break H4, which will need to change
    ESL_SSE() autoconf macro call to ESL_SSE4(), eslENABLE_SSE ->
    eslENABLE_SSE4, and suchlike.
Commits on Jun 4, 2018
  1. fixes intermittent glitch in esl_buffer_utest detected by valgrind

    cryptogenomicon committed Jun 4, 2018
    esl_buffer.c::buffer_counttok line ~1859 checks for \r\n newline,
    because it may need to back nc up by one. However, if input ends with
    token, [bf->pos+nc] is off the end of the input, so the test for \n
    there needs some protection. Add check for bf->pos+nc < bf->n.
Commits on Jun 2, 2018
Commits on Jun 1, 2018
  1. Reinstates valgrind esl_buffer_utest.

    cryptogenomicon committed Jun 1, 2018
    This test had been disabled in testsuite.sqc because it tickled
    valgrind bug #258294 on OS/X for valgrind <= 3.6.1. Now looks like
    valgrind's been fixed (I'm using 3.14.0.GIT master head).
  2. Fixes gcc-8 compiler warnings in esl_dsqdata utest snprintf()'s.

    cryptogenomicon committed Jun 1, 2018
    Compiler couldn't tell that tmpfile[32] could be safely written to
    basename[32] with a suffix, because tmpfile only contains a short
    tmpfile name. Changed tmpfile[32] to [16].
Commits on May 30, 2018
  1. Removes outdated 00CHECKLIST, and INSTALL.

    cryptogenomicon committed May 30, 2018
    Also, edits in LICENSE and README.md. Avoid using sedition, so github
    clone and distro tarball are nigh-identical.
  2. Updates dates for HMMER release 3.2.

    cryptogenomicon committed May 30, 2018
    Also fixes some manpage font problems, detected by badman.py
Commits on May 29, 2018
Commits on May 2, 2018
Commits on May 1, 2018
Commits on Apr 21, 2018
  1. Fixes bug in ESL_AVX512 configure macro that could overwrite CFLAGS.

    cryptogenomicon committed Apr 21, 2018
    This is the same one-line fix as in commit 745a9a1 on the release-0.44
    branch. I'd meant to apply it to `develop`, where Nick is working.
    Don't want to merge release-0.44's other changes back yet, so decided
    it was easier to just make the same change as a separate commit. Watch
    out for this on merge, but it should be fine.
Commits on Apr 20, 2018
Commits on Apr 3, 2018
  1. Overhauls how 'make install' works.

    cryptogenomicon committed Apr 3, 2018
    Now Easel only installs miniapps and their man pages.  It no longer
    installs .h headers or libeasel.a. We've really never used it that
    way.
    
    Variable substitutions in man pages (EASEL_VERSION, etc) are now done
    by ./configure, not by outmoded sedition script. Updated man page
    headers and trailers, made consistent with HMMER style.
    
    'make install' is now always verbose; quiet beautifications removed.
    
    Removed 'make dist'.
    
    Removed ifneq's from Makefiles. Aiming to have a checkout of github
    master branch act identically to a tarball, which means we won't
    remove any directories or modify any files when we make a release
    tarball. This makes the ifneq checks for documentation/, etc obsolete.
    
    Removed LICENSE.sh and LICENSE.tag.
Commits on Feb 22, 2018
Commits on Feb 21, 2018
Commits on Feb 2, 2018
  1. Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D().

    cryptogenomicon committed Feb 2, 2018
    Adds esl_free(), which allows ptr to be NULL. This is actually
    unnecessary. C99 free() accepts NULL as a no-op.
    
    Adds esl_msa_Sizeof(), which I intend to use to pull some alirecsize
    capability into esl-alistat. Also, utest_Sizeof() unit test for it.
    
    [SRE:H4/146]
Commits on Feb 1, 2018
  1. Fixes compilation warnings from esl_sqio_ncbi on recent OS/X.

    cryptogenomicon committed Feb 1, 2018
    esl_sqio_ncbi code manipulates both text-mode and digital-mode
    sequences with the same <ptr> variable. Because it can assign
    eslDSQ_SENTINEL (255) to *ptr, ptr needs to be declared unsigned char.
Commits on Nov 2, 2017
Commits on Aug 22, 2017
Commits on Aug 21, 2017
  1. Improves example driver for esl_scorematrix

    cryptogenomicon committed Aug 21, 2017
    Adds getopts, including --dna option for reading DNA matrices.
Commits on Aug 9, 2017
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