EddyRivasLab hmmer issues

EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs

http://hmmer.org

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issues

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hmmalign --mapali fails if msa contains fragments

#83 traviswheeler closed 7 years ago
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jackhmmer segfaults if target seqdb contains duplicate names

#82 traviswheeler closed 7 years ago
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hmm->compo calculation was wrong, bug in iocc[] calculation

#81 traviswheeler closed 7 years ago
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hmmbuild gives cryptic error on msa containing internal ~ chars

#80 traviswheeler closed 7 years ago
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hmmscan --tblout segfaults if HMM lacks accession/description

#79 traviswheeler closed 7 years ago
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hmmalign fails on some seqs: Decoding ERANGE error

#78 traviswheeler closed 7 years ago
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H2 models produced by H2 hmmconvert aren't readable

#77 traviswheeler closed 7 years ago
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hmmscan output of HMM names/descriptions corrupted somehow

#76 traviswheeler closed 7 years ago
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hmmpress -f corrupts HMM database instead of overwriting it

#75 traviswheeler closed 7 years ago
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traces containing X (fragments) are misaligned

#74 traviswheeler closed 7 years ago
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stotrace unit test may fail on i686 platforms

#73 traviswheeler closed 7 years ago
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hmmscan segfaults on sequences containing * characters

#72 traviswheeler closed 7 years ago
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hmmscan --cut_{ga,nc,tc} fails to impose correct thresholds

#71 traviswheeler closed 7 years ago
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hmmbuild --mpi fails to record GA,TC,NC thresholds

#70 traviswheeler closed 7 years ago
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seq descriptions containing '%' cause segfault

#69 traviswheeler closed 7 years ago
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hmmscan tabular domain output reverses target, query lengths

#68 traviswheeler closed 7 years ago
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jackhmmer fails: "backconverted subseq didn't end at expected length"

#67 traviswheeler closed 7 years ago
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hmmbuild fails trace validation on frag-rich MSA

#66 traviswheeler closed 7 years ago
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hmmbuild fails to build reasonable model on frag-rich MSA

#65 traviswheeler closed 7 years ago
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hmmpress fails in ftello() on a large HMM database.

#64 traviswheeler closed 7 years ago
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hmmalign --trim memory faults

#63 traviswheeler closed 7 years ago
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hmmscan seg faults in rare cases trying to output per-sequence hit

#62 traviswheeler closed 7 years ago
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hmmconvert -2 creates an invalid HMMER2 model if ali len > 9999

#61 traviswheeler closed 7 years ago
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hmmbuild -n (assign name to HMM) option doesn't have any effect

#60 traviswheeler closed 7 years ago
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domain definition finds same domain twice

#59 traviswheeler closed 7 years ago
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Degenerate residues cause target seq to be bias-filtered.

#58 traviswheeler closed 7 years ago
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jackhmmer -A segfaults.

#57 traviswheeler closed 7 years ago
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hmmscan --cut_ga segfaults

#56 traviswheeler closed 7 years ago
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Zero length sequences crash hmmscan

#55 traviswheeler closed 7 years ago
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Compiler "option -xk not supported" warnings on MacOS/X

#54 traviswheeler closed 7 years ago
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"non-aligned pointer being freed" on MacOS/X x86_64 icc

#53 traviswheeler closed 7 years ago
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Low information content models have poor sensitivity

#52 traviswheeler closed 7 years ago
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hmmbuild --enone reports duplicate lines in header

#51 traviswheeler closed 7 years ago
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Different runs of hmmsearch give different answers.

#50 traviswheeler closed 7 years ago
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hmmsearch faults when reading alignment file.

#49 traviswheeler closed 7 years ago
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hmmscan failed to report some hits (rarely).

#48 traviswheeler closed 7 years ago
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hmmfetch failed on hmmpress'ed HMM files.

#47 traviswheeler closed 7 years ago
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hmmscan gave error message of (null).

#46 traviswheeler closed 7 years ago
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jackhmmer crashed because code wasn't done.

#45 traviswheeler closed 7 years ago
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hmmbuild -o crashes if alignment has #=GR SS or #=GR SA lines

#44 traviswheeler closed 7 years ago
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ExtremeValueFitHistogram() crashes on uncensored fitting

#43 traviswheeler closed 7 years ago
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hmmalign can't handle length 0 sequences

#42 traviswheeler closed 7 years ago
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Malloc failure in hmmsearch

#41 traviswheeler closed 7 years ago
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get_wee_midpt crashes out if given seq of L=1

#40 traviswheeler closed 7 years ago
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hmmsearch does not scale on SMP Xeons with hyperthreads

#39 traviswheeler closed 7 years ago
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P7Forward typo: bsc[M-1] should be bsc[M]

#38 traviswheeler closed 7 years ago
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Negative element in dsq; char vs. unsigned char.

#37 traviswheeler closed 7 years ago
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Memory crash in hmmpfam.

#36 traviswheeler closed 7 years ago
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Memory-related hmmsearch crash on Swissprot.

#35 traviswheeler closed 7 years ago
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Does not use CPPFLAGS, LDFLAGS in environment

#34 traviswheeler closed 7 years ago
0

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