New upstream version 2.5j+dfsg (41773b3c) · Commits · Debian Med / hmmer2

.gitignore

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Original line number	Diff line number	Diff line
		*.o
		afetch
		alistat
		compalign
		compstruct
		libsquid.a
		revcomp
		seqsplit
		seqstat
		sfetch
		shuffle
		sindex
		sreformat
		translate
		weight
		hmmalign
		hmmbuild
		hmmcalibrate
		hmmconvert
		hmmemit
		hmmfetch
		hmmindex
		hmmpfam
		hmmsearch
		libhmmer.a
		alignalign_test
		evd_test
		masks_test
		parsingviterbi_test
		tophits_test
		trace_test
		viterbi_exercise
		weeviterbi_test
		sreaa*
		*.OPT.HMM.ssi
		hmmalign2
		hmmbuild2
		hmmcalibrate2
		hmmconvert2
		hmmemit2
		hmmfetch2
		hmmindex2
		hmmpfam2
		hmmsearch2
		libhmmer2.so
		hmmalign
		hmmbuild
		hmmcalibrate
		hmmconvert
		hmmemit
		hmmfetch
		hmmindex
		hmmpfam
		hmmsearch
		libhmmer.so

Bugs/BUGTRAX

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Original line number	Diff line number	Diff line
		ID 1
		STATUS closed
		DESCRIPTION BPA1_HUMAN crashes Pfam server
		NOTED_DATE 1/16/98
		NOTED_XREF
		REPORTED_BY David Kerk
		REPRODUCE_WITH
		REPRODUCE_ON ANY
		CLOSED_DATE 1/16/98
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 2
		STATUS closed
		DESCRIPTION null2 consistency problem between per-seq and per-domain
		NOTED_DATE 1/7/99
		NOTED_XREF notebook STL1 p.117
		REPORTED_BY David Kerk
		REPRODUCE_WITH bug2.pl
		REPRODUCE_ON ANY
		CLOSED_DATE SRE, Tue Dec 19 17:45:46 2000
		CLOSED_XREF STL3 notebook, p.127
		CLOSED_ACTION created postprocess_hit() in hmmpfam.c
		//
		ID 3
		STATUS closed
		DESCRIPTION hmmbuild segfaults on alignments labeled with #=ID
		NOTED_DATE 1/15/99
		NOTED_XREF
		REPORTED_BY SRE
		REPRODUCE_WITH
		REPRODUCE_ON Solaris
		CLOSED_DATE 1/19/99
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 4
		STATUS closed
		DESCRIPTION sreformat core dumps when reformatting single seq to SELEX
		NOTED_DATE 1/18/99
		NOTED_XREF
		REPORTED_BY sre
		REPRODUCE_WITH
		REPRODUCE_ON any
		CLOSED_DATE 1/19/99
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 5
		STATUS closed
		DESCRIPTION hmmbuild core dumps when building model from single
		seqs FASTA file
		NOTED_DATE 1/18/99
		NOTED_XREF
		REPORTED_BY agb
		REPRODUCE_WITH
		REPRODUCE_ON
		CLOSED_DATE 1/19/99
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 6
		STATUS closed
		DESCRIPTION getseq clashes with GCG program of same name
		NOTED_DATE 1/18/99
		NOTED_XREF
		REPORTED_BY sre
		REPRODUCE_WITH
		REPRODUCE_ON n/a
		CLOSED_DATE 1/19/99
		CLOSED_XREF
		CLOSED_ACTION renamed getseq to sfetch
		//
		ID 7
		STATUS closed
		DESCRIPTION Digital 4.0d binaries do not run on 4.0b;
		pthread_setconcurrency() missing
		NOTED_DATE 1/18/99
		NOTED_XREF
		REPORTED_BY Bill Pearson
		REPRODUCE_WITH
		REPRODUCE_ON Digital UNIX
		CLOSED_DATE 1/19/99
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 8
		STATUS closed
		DESCRIPTION hmmpfam segfaults on GCG-reformatted Swissprot file
		NOTED_DATE 1/19/99
		NOTED_XREF
		REPORTED_BY James Holzwarth
		REPRODUCE_WITH
		REPRODUCE_ON
		CLOSED_DATE 1/19/99
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 9
		STATUS OPEN
		DESCRIPTION C->T transition doesn't seem to be parsed from save files
		NOTED_DATE 6/29/99
		NOTED_XREF
		REPORTED_BY Bob Farrington
		REPRODUCE_WITH
		REPRODUCE_ON
		CLOSED_DATE
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 10
		STATUS closed
		DESCRIPTION Floating point exception in ExtremeValueP() on Digital 4.0b:
		range error.
		NOTED_DATE 7/2/99
		NOTED_XREF
		REPORTED_BY ju@harvard
		REPRODUCE_WITH
		REPRODUCE_ON Digital UNIX 4.0b
		CLOSED_DATE 9/17/99
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 11
		STATUS OPEN
		DESCRIPTION hmmbuild, illegal B->E in traceback
		NOTED_DATE 11/15/99
		NOTED_XREF
		REPORTED_BY marcel@cs.berkeley.edu
		REPRODUCE_WITH
		REPRODUCE_ON
		CLOSED_DATE
		CLOSED_XREF
		CLOSED_ACTION
		//
		ID 12
		STATUS closed
		DESCRIPTION --domE, --domT don't work correctly in hmmpfam; E-value
		is assumed to be monotonic w/ score.
		NOTED_DATE 11/29/00
		NOTED_XREF STL3 p.127
		REPORTED_BY vanschlun@gcg.com
		REPRODUCE_WITH bug12.pl
		REPRODUCE_ON any
		CLOSED_DATE SRE, Tue Dec 19 17:47:01 2000
		CLOSED_XREF STL3 p.127
		CLOSED_ACTION removed the break statements when looping over domain list.
		//
		ID 13
		STATUS closed
		DESCRIPTION hmmconvert happily converts a bogus HMM database w/
		both DNA and protein
		NOTED_DATE 12/24/00
		NOTED_XREF STL3 p.133
		REPORTED_BY vanschlun@gcg.com, email 12/14/00
		REPRODUCE_WITH bug13.pl
		REPRODUCE_ON any
		CLOSED_DATE SRE, Sun Dec 24 11:58:28 2000
		CLOSED_XREF STL3 p.133
		CLOSED_ACTION hmmio.c now checks for changes in Alphabet_type while reading HMMs.
		//
		ID 14
		STATUS closed
		DESCRIPTION hmmconvert doesn't complain about appending binary to
		ASCII HMMs, or vice versa
		NOTED_DATE 12/24/00
		NOTED_XREF STL3 p.133
		REPORTED_BY vanschlun@gcg.com, email 12/14/00
		REPRODUCE_WITH bug13.pl
		REPRODUCE_ON any
		CLOSED_DATE SRE, Sun Dec 24 15:33:11 2000
		CLOSED_XREF STL3 p. 133
		CLOSED_ACTION hmmconvert.c now tests for this case
		//
		ID 15
		STATUS untested
		DESCRIPTION hmmpfam slave process leak when nhmm < nslaves
		NOTED_DATE 10/25/01
		NOTED_XREF STL5 p. 66
		REPORTED_BY John Blanchard (johnb@incyte.com), email 10/17/01
		REPRODUCE_WITH
		REPRODUCE_ON any PVM
		CLOSED_DATE
		CLOSED_XREF STL5 p.66
		CLOSED_ACTION hmmpfam.c modified: kill slaves off in a separate loop
		//
		ID 16
		STATUS untested
		DESCRIPTION PVMConfirmSlaves() assumes nslaves=nhosts
		NOTED_DATE 10/25/01
		NOTED_XREF STL5 p. 66
		REPORTED_BY John Blanchard (johnb@incyte.com), email 10/17/01
		REPRODUCE_WITH
		REPRODUCE_ON any PVM; only when DEBUGLEVEL>0
		CLOSED_DATE
		CLOSED_XREF STL5 p.66
		CLOSED_ACTION pvm.c:PVMConfirmSlaves()... replace pvm_config() w/ pvm_tasks().
		//
		ID 17
		STATUS closed
		DESCRIPTION threaded, unthreaded hmmsearch don't give same histogram
		NOTED_DATE 2/27/02
		NOTED_XREF STL6 p.1
		REPORTED_BY Yang Yang
		REPRODUCE_WITH bug17.sh
		REPRODUCE_ON any
		CLOSED_DATE 2/27/02
		CLOSED_XREF STL6 p.1
		CLOSED_ACTION modifications to hmmsearch.c; see notes.
		//
		ID 18
		STATUS closed
		DESCRIPTION HMMs differ when built from mul vs. Stockholm format
		NOTED_DATE 3/16/02
		NOTED_XREF STL6 p.12
		REPORTED_BY Sam Griffiths (sjg@sanger.ac.uk)
		REPRODUCE_WITH bug18.sh - was deleted from CVS.
		REPRODUCE_ON Alpha (waterbug)
		CLOSED_DATE 3/29/02
		CLOSED_XREF STL6 p.12
		CLOSED_ACTION Not a bug.
		//
		ID h19
		TITLE floating point exception on Alpha/Linux
		STATUS CLOSED
		XREF none
		REPORTED_BY "Yungok S. Ihm" <youngok@iastate.edu>
		CLOSED_DATE SRE, Fri May 9 15:31:23 2003
		DESCRIPTION
		hmmpfam crashes on extremely low scoring hits (<-1000),
		on Alpha/Linux. Appears in both 2.2g and 2.3dev.
		mathsupport.c:PValue() doesn't check for underflow before
		calling sreEXP2() on the score; the Alpha crashes on this.
		No test case built for bugs.sqc.
		//
		ID h20
		TITLE hmmpfam E-values dependent on # of threads.
		STATUS CLOSED
		XREF STL7 p.70
		REPORTED_BY Robert A. Wilson <robwilso@us.ibm.com>
		CLOSED_DATE SRE, Fri Jun 6 18:56:43 2003
		DESCRIPTION
		Original report cited difference in E-values between
		IBM 2.2g binaries and 2.3 binaries. Investigation shows
		problem is really in both: # of threads is added to
		nhmms, and counted as Z, so E-values end up depending
		on thread #. (IBM 2.2g binaries weren't compiled w/ threads,
		hence the difference seen by IBM.) In hmmpfam.c:worker_thread(),
		we were bumping nhmm++ before successfully reading the HMM,
		so on normal exit, each thread bumps nhmm one extra time after
		the HMM file is emptied.

		To reproduce: hmmpfam --cpu 0 <any hmm> <any seq> vs.
		hmmpfam --cpu <n> <any hmm> <any seq>
		should give identical E-values.
		Fixed; verified on Intel/Linux.
		No test case built for bugs.sqc.
		//
		ID h21
		TITLE "make install" doesn't create target directories
		STATUS CLOSED
		XREF STL7 p.70
		REPORTED_BY Gisle Slensminde <gisle@ii.uib.no> [10 Jun 2003]
		CLOSED_DATE SRE, Thu Jun 12 12:37:54 2003
		DESCRIPTION
		"make install" doesn't create target directories if they
		don't exist, and fails w/ poor error message. Added and documented
		mkdir -p steps in Makefile.in
		//
		ID h22
		TITLE hmmpfam crash related to resizing DP matrix
		STATUS CLOSED
		XREF STL7 p.70
		REPORTED_BY James Cuff <james@sanger.ac.uk> 12 June 2003
		CLOSED_DATE SRE, Fri Jun 13 14:56:42 2003
		DESCRIPTION
		hmmpfam crashes on Pfam_ls.
		Problem is with reallocation in ResizePlan7Matrix(), when it
		is called with N < maxN - it didn't reinitialize ptrs up to
		maxN, it only did it up to N.
		//
		ID h23
		TITLE Does not compile w/ --enable-pvm
		STATUS CLOSED
		XREF STL7 p.71
		REPORTED_BY Goran Ceric <goran@genetics.wustl.edu> 12 June 2003
		CLOSED_DATE SRE, Fri Jun 13 14:57:58 2003
		DESCRIPTION
		Didn't compile w/ PVM support, because of #define name changes
		in 2.3.
		//
		ID h24
		TITLE Does not use CPPFLAGS, LDFLAGS in environment
		STATUS CLOSED
		XREF STL7 p.71
		REPORTED_BY Ajay Khanna <askhanna@genetics.wustl.edu> 13 June 2003
		CLOSED_DATE SRE, Fri Jun 13 14:59:13 2003
		DESCRIPTION
		./configure claims to use CPPFLAGS, LDFLAGS from environment,
		but doesn't.
		//
		ID h25
		TITLE Memory-related hmmsearch crash on Swissprot.
		STATUS CLOSED
		XREF STL7 p.121
		REPORTED_BY Niklaus Fankhauser <niklaus.fankhauser@izb.unibe.ch> 26 Sept 2003;
		Kaivalya Dixit <dixit@austin.ibm.com>, 24 Sept 2003.
		OPENED_DATE SRE, Tue Sep 30 14:53:19 2003
		CLOSED_DATE SRE, Wed Oct 1 08:07:18 2003
		DESCRIPTION
		hmmsearch crashes unpredictably on Swissprot searches (EMBL
		format).

		AMD contributes an Insure++ report showing three problems:
		1. Alphabet[] is not a string but is being passed to strchr();
		2. readEMBL is looking for a \0 in a growing seq, but a growing
		seq has no \0 until ReadSeq() polishes it off;
		3. xmx[] is shown as a dangling/wild ptr in core_algorithms.c
		and fast_algorithms.c.
		AMD and/or Intel also indicate, via Kaivalya, that the problem
		is in sqio.c: they explicitly nul-terminate after every reallocation
		of the seq, and the problem disappears.
		Fixed problems 1 and 2. Can't find the problem that Insure++ is
		bitching about for 3; worrying. Bug goes away: it was clearly the result
		of problem 2. Bugs in #1 should only appear for databases with
		nonstandard residues.
		//
		ID h26
		TITLE Memory crash in hmmpfam.
		STATUS CLOSED
		XREF STL7 p.122.
		REPORTED_BY Gary Montry <montry@spsoft.com>, 15 Aug 2003.
		OPENED_DATE SRE, Wed Oct 1 12:29:25 2003
		CLOSED_DATE SRE, Thu Oct 2 11:20:00 2003
		DESCRIPTION
		hmmpfam search with 125,000aa sequence eventually crashes
		because of lack of RAM, instead of successfully using small
		memory routines.

		Problem is that the code assumed that M,N can't both grow in
		allocating a matrix, but that's not true in hmmpfam; after P7SmallViterbi(),
		we may hand various sized bits of sequence off for subalignment,
		with different sized models.

		Wrote P7ViterbiSpaceOK(); used it instead of P7ViterbiSize() to switch
		between normal and small variants; allow creation routine to grow in M
		and N (padM and padN can both be positive); make initial allocs for
		hmmpfam matrices to be 300x300, to avoid pathologically asymmetric
		matrices.
		//
		ID h27
		TITLE Negative element in dsq; char vs. unsigned char.
		STATUS CLOSED
		XREF STL7 p.123
		REPORTED_BY Kaivalya Dixit <dixit@austin.ibm.com>, Sept 2003.
		OPENED_DATE SRE, Thu Oct 2 2003
		CLOSED_DATE SRE, Thu Oct 2 11:25:57 2003
		DESCRIPTION
		Turned up in SPEC certification process. Alan L. MacKay
		<amackay@us.ibm.com>, of IBM AIX Compilers/Performance group, sends
		an Insure++ report that shows a case where dsq[] was a negative
		number. Kaivalya reports that they "fixed" this by forcing compilers
		to use unsigned chars by default. A confusing discussion ensues;
		MacKay thinks the problem is the use of char dsq[] as an array index,
		whereas I think the code "guarantees" nonnegative dsq[] and that
		there isn't a problem here; I think the crash IBM saw was coming
		from memory corruption due to bug #h25.

		Nonetheless, he has a point: if I'm going to use dsq[] as an array
		index, it would be better coding practice to declare it as
		unsigned char.

		Changed dsq from char to unsigned char throughout (and some
		instances of sym, symidx). Removed (int) casts whereever dsq[],
		symidx were being used as array indices.
		//
		ID h28
		TITLE P7Forward typo: bsc[M-1] should be bsc[M]
		STATUS CLOSED
		XREF STL7 p.123
		REPORTED_BY Robel Kahsay <kahsay@mail.capsl.udel.edu>
		CLOSED_DATE SRE, Fri Oct 3 12:48:50 2003
		DESCRIPTION
		Calculation of mmx[M] should touch bsc[M], not bsc[M-1].
		//
		ID h29
		TITLE hmmsearch does not scale on SMP Xeons with hyperthreads
		STATUS CLOSED
		XREF notebook/0115-hmmer-bug-h29
		REPORTED_BY Gordon Gremme <gremme@zbh.uni-hamburg.de>
		OPENED_DATE SRE, Thu Jan 15 13:30:00 2004
		CLOSED_DATE SRE, Thu Jan 15 15:43:25 2004
		DESCRIPTION
		See the notes [xref] for details.

		This appears to be a Linux 2.4 SMP scheduler problem.
		No action taken.
		//
		ID h30
		TITLE get_wee_midpt crashes out if given seq of L=1
		STATUS CLOSED
		XREF 2004:1119-hmmer-bug-h30
		REPORTED_BY James Stroud <jstroud@mbi.ucla.edu>
		OPENED_DATE SRE, Fri Nov 19 13:28:55 2004
		CLOSED_DATE SRE, Fri Nov 19 13:58:08 2004
		DESCRIPTION
		hmmpfam crashes on Pfam_fs w/ "FATAL: you can't init get_wee_midpt
		with a T", on a long HMM Arena_RNA_pol.

		The problem is that P7WeeViterbi() is called w/ subseq of L=1. The
		init of P7WeeViterbi sets begin,end points initially to STS, STT;
		but when 1==L, assignment of tassign[L] to STT clobbers tassign[1].

		Fixing this properly will require rethinking get_wee_midpt carefully.

		Instead, hack around it. P7WeeViterbi() is only called once, from
		within P7SmallViterbi(). Insert an extra test; if sqlen==1, do not
		call P7WeeViterbi(), instead allocate a tiny L=1 matrix and use
		P7Viterbi().

		Document P7WeeViterbi(): it can't take L=1.
		//

Bugs/bug11.msf

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Bugs/bug12-ELAV_DROME

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		>ELAV_DROME ELAV PROTEIN (EMBRYONIC LETHAL ABNORMAL VISUAL PROTEIN).
		MDFIMANTGAGGGVDTQAQLMQSAAAAAAVAATNAAAAPVQNAAAVAAAA
		QLQQQQVQQAILQVQQQQTQQAVAAAAAAVTQQLQQQQQAVVAQQAVVQQ
		QQQQAAAVVQQAAVQQAVVPQPQQAQPNTNGNAGSGSQNGSNGSTETRTN
		LIVNYLPQTMTEDEIRSLFSSVGEIESVKLIRDKSQVYIDPLNPQAPSKG
		QSLGYGFVNYVRPQDAEQAVNVLNGLRLQNKTIKVSFARPSSDAIKGANL
		YVSGLPKTMTQQELEAIFAPFGAIITSRILQNAGNDTQTKGVGFIRFDKR
		EEATRAIIALNGTTPSSCTDPIVVKFSNTPGSTSKIIQPQLPAFLNPQLV
		RRIGGAMHTPVNKGLARFSPMAGDMLDVMLPNGLGAAAAAATTLASGPGG
		AYPIFIYNLAPETEEAALWQLFGPFGAVQSVKIVKDPTTNQCKGYGFVSM
		TNYDEAAMAIRALNGYTMGNRVLQVSFKTNKAK

Bugs/bug12-minipfam

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