Revisions of hmmer3
Dmitry Roshchin (Dmitry_R)
accepted
request 1036523
from
Stefan Brüns (StefanBruens)
(revision 6)
- Update to version 3.3.2 * Fixed a recently introduced bug that could cause hmmsearch (and presumably hmmscan) to segfault on rare comparisons involving highly biased sequences. * ./configure –enable-PIC wasn’t setting -fPIC option in impl-sse, impl-vmx Makefiles. * fixed an uninitialized ptr in makehmmerdb, in the fm_data structure, which could cause makehmmerdb to crash.
Ismail Dönmez (namtrac)
accepted
request 617033
from
Luigi Baldoni (alois)
(revision 4)
- Update to version 3.2.1 * iss #142: compilation fails ungracefully on unsupported ppc64le * iss #140: jackhmmer --fast segfault. Removes --fast and --symfrac options from jackhmmer and its documentation. * iss #141, #120: compilation failures on i586, ppc64be. * iss #132: hmmbuild miscounts transitions in final node.
Atri Bhattacharya (badshah400)
accepted
request 615432
from
Luigi Baldoni (alois)
(revision 3)
- Update to version 3.2 Larger changes: * HMMER is now distributed under the BSD license, instead of the GPL. * The 'make install' has been streamlined. Now we install only programs and man pages, for 18 HMMER programs and 22 Easel miniapps. We don't install development .h headers or .a libraries. * We changed our default policy on the number of threads/cores that the search programs use. Previously multithreaded programs would use all available cores by default; now we use two worker threads by default (~2 cores), if multiple cores are available. HMMER3 search programs do not scale much beyond 2 cores anyway, due to input saturation and memory use. * H3 now strictly requires either SSE2 or Altivec/VMX vector support. The portable 'dummy' implementation has been removed. This was an non-vectorized portable pure C implementation, much slower than HMMER3 on x86 and PowerPC platforms with SSE2 or Altivec/VMX vector instructions. We had included it because we could -- HMMER3 implements "generic" non-vectorized versions of its core algorithms for unit testing purposes anyway. We thought maybe it'd be useful. As far as I can tell, it was never useful, but several packagers on non-x86, non-PowerPC platforms packaged and distributed it, ignoring the prominent health warnings we put on it. Smaller new features include: * improved documentation of --mxfile and score matrix file format * adds support for EBI's "uncheck all hits" on jackhmmer web site * removed experimental hmmbuild --seq_weights_r and --seq_weights_e options * appeased new gcc6 --Wmisleading-indentation warning * SSI indexing is now robust against duplicate keys * autoconf now robust against someone running gnu `autoheader` * improved autoconf of SIMD vector support * improved autoconf of DAZ,FTZ support on x86 processors * improved autodetection of phylip interleaved vs sequential format * improved autodetection of A2M vs. aligned FASTA format * clarified A2M format parse error when file contains 'O' residue * improved portability to Intel/Solaris * FASTA parser now ignores description line after a ctrl-A * MSAs output with -A option now include name, acc, desc, author markup. * In Easel miniapps, esl-translate replaces previous (buggy) esl-stranslate. * Easel miniapps include esl-alirev, reverse complementing RNA/DNA alignment * nhmmer/nhmmscan now allow alignments as target dbs * target relentropy for DNA models changed from 0.45 to 0.62 * updated the User Guide Fixed bugs include: * nhmmscan faulted on old model files because it expected MAXL field * --cut-ga wasn't checking that GA line was actually present in model * GA thresholds weren't being captured from DNA/RNA Stockholm alignments * A2M alignment parsing was corrupted on lines ending in insertions * alphabet-guessing failed for FASTA seq >4096 bytes and <4000 residues * genbank to fasta format conversion was leaving extra \n in accession * NCBI db format: multithreaded nhmmer was failing to read * NCBI db format: 1st database sequence was skipped for second query (#e6) * unit test failures in esl_normal, esl_random due to floating point math * nhmmer was corrupted by * symbols in input sequence (iss#118) * hmmsearch -A crashed if top-ranked hit has no domains (iss#131) * new variety of "backconverted subseq" hmmsearch crash on *'s (iss#135) * qsort() callbacks now return -1/0/1 as they should. (Infernal iss#11) * esl_buffer hangs when input ends with \r (Easel iss#23) - Dropped hmmer-bufferoverflowstrncat.patch (merged upstream) - Dropped devel subpackage (easel no longer installs header files and static library)
Matthias Mailänder (Mailaender)
accepted
request 436102
from
Luigi Baldoni (alois)
(revision 2)
Update to latest released version.
Dmitry Roshchin (Dmitry_R)
accepted
request 375894
from
Matthias Mailänder (Mailaender)
(revision 1)
Displaying all 6 revisions