.gitignore

+configure
+easel
+hmmer
\ No newline at end of file

INSTALL

 Brief installation instructions 
-Infernal 1.1.2; July 2016
+Infernal 1.1.3; Nov 2019
 -------------------------------------------------------------
 
 These are quick installation instructions. For complete documentation,
 including customization and troubleshooting, please see the
 Installation chapter in the Infernal User's Guide (Userguide.pdf).
 
-Starting from a source distribution, infernal-1.1.2.tar.gz:
- uncompress:                uncompress infernal-1.1.2.tar.gz  
- unpack:                    tar xf infernal-1.1.2.tar
- move into new directory:   cd infernal-1.1.2
+Starting from a source distribution, infernal-1.1.3.tar.gz:
+ uncompress:                uncompress infernal-1.1.3.tar.gz  
+ unpack:                    tar xf infernal-1.1.3.tar
+ move into new directory:   cd infernal-1.1.3
  configure:                 ./configure
  build:                     make
  automated tests:           make check
@@ -26,7 +26,7 @@ on most modern processors. Infernal requires either an x86-compatible
 (IA32, IA64, or Intel64) processor that supports the SSE2 vector
 instruction set, or a PowerPC processor that supports the Altivec/VMX
 instruction set. If your platform does not support one of these vector
-instruction sets, you won’t be able to install and run Infernal 1.1 on
+instruction sets, you won't be able to install and run Infernal 1.1 on
 it.
 
 -------------------------------------------------------------

LICENSE

 Infernal - inference of RNA secondary structural alignments
-@INFERNAL_COPYRIGHT@
-Copyright (C) 1991-2016      Sean R. Eddy
-Copyright (C) 2005-2016      Eric P. Nawrocki
+Copyright (C) 1991-2019      Sean R. Eddy
+Copyright (C) 2005-2019      Eric P. Nawrocki
 Copyright (C) 2005-2011      Diana L. Kolbe
 Copyright (C) 2004           Zasha Weinberg
 Copyright (C) 1990           Don G.Gilbert
-Copyright (C) 2000-2016      Howard Hughes Medical Institute
+Copyright (C) 2000-2019      Howard Hughes Medical Institute
 Copyright (C) 1995-2006      Washington University School of Medicine
 Copyright (C) 1992-1995      MRC Laboratory of Molecular Biology
 Copyright (C) 2004           University of Washington, Seattle

Makefile.in

@@ -21,13 +21,8 @@ srcdir         = @srcdir@
 VPATH          = @srcdir@
 SHELL          = /bin/sh
 
-# location of easel
 ESLDIR         = @INFERNAL_ESLDIR@
-
-# location of hmmer
 HMMERDIR       = @INFERNAL_HMMERDIR@
-
-# location of suffix array library
 SADIR          = @INFERNAL_SADIR@
 
 # impl directory (currently only either 'impl_sse' or '')
@@ -58,7 +53,6 @@ man1ext     = .1
 CC        = @CC@
 CFLAGS    = @CFLAGS@
 LDFLAGS   = -static @LDFLAGS@
-SIMDFLAGS = @SIMD_CFLAGS@
 CPPFLAGS  = @CPPFLAGS@
 
 # Other tools
@@ -131,46 +125,20 @@ tests:
 # We do a 'check' in HMMERDIR/testsuite, not HMMERDIR/ because we
 # don't need to run the Easel testsuite twice.
 #
-
-# Also, HMMER's 'make check' requires its own easel subdir complete
-# with compiled miniapps. This may or may not exist. In working copies
-# of the trunk it will exist but won't be compiled (infernal/hmmer/
-# will use infernal/easel, not infernal/hmmer/easel). In a released
-# version infernal/hmmer/easel won't even exist since we delete it
-# prior to creating a release.  So, we take care to have the calling
-# of hmmer's testsuite work in either case. If hmmer/easel/ exists we
-# copy the required miniapps into it and run 'make check' from
-# hmmer/testsuite then delete them. If it doesn't, we create a symlink
-# to infernal/easel as infernal/hmmer/easel then we run the testsuite
-# and then we delete the symlink. Also, if srcdir/hmmer/easel doesn't
-# exist, we symlink it to srcdir/easel because the hmmer testsuite
-# needs easel/formats/BLOSUM62 which will only be in srcdir/easel
-# (yuck!).
-
 check:
+	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}${ESLDIR}              ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${SADIR}               ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}${HMMERDIR}            ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}src                    ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${ESLDIR}              ${QUIET_SUBDIR1} check
-	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-afetch;   then cp ${ESLDIR}/miniapps/esl-afetch   ${HMMERDIR}/easel/miniapps; fi
-	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-reformat; then cp ${ESLDIR}/miniapps/esl-reformat ${HMMERDIR}/easel/miniapps; fi
-	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-sfetch;   then cp ${ESLDIR}/miniapps/esl-sfetch   ${HMMERDIR}/easel/miniapps; fi
-	if   test -d ${HMMERDIR}/easel && ! test -e  ${HMMERDIR}/easel/miniapps/esl-sfetch;   then cp ${ESLDIR}/miniapps/esl-shuffle  ${HMMERDIR}/easel/miniapps; fi
-	if ! test -d ${HMMERDIR}/easel; then cd ${HMMERDIR}; @LN_S@ ../${ESLDIR} .; cd ..; fi
-	if ! test -d ${srcdir}/${HMMERDIR}/easel; then @LN_S@ ${srcdir}/${ESLDIR} ${srcdir}/${HMMERDIR}/easel; fi
 	${QUIET_SUBDIR0}${HMMERDIR}/testsuite  ${QUIET_SUBDIR1} check
-	if   test -L ${HMMERDIR}/easel; then rm ${HMMERDIR}/easel; fi
-	if   test -L ${srcdir}/${HMMERDIR}/easel; then rm ${srcdir}/${HMMERDIR}/easel; fi
-	if   test -e ${HMMERDIR}/easel/miniapps/esl-afetch;   then rm ${HMMERDIR}/easel/miniapps/esl-afetch;   fi
-	if   test -e ${HMMERDIR}/easel/miniapps/esl-reformat; then rm ${HMMERDIR}/easel/miniapps/esl-reformat; fi
-	if   test -e ${HMMERDIR}/easel/miniapps/esl-sfetch;   then rm ${HMMERDIR}/easel/miniapps/esl-sfetch;   fi
-	if   test -e ${HMMERDIR}/easel/miniapps/esl-shuffle;  then rm ${HMMERDIR}/easel/miniapps/esl-shuffle;  fi
 	${QUIET_SUBDIR0}testsuite              ${QUIET_SUBDIR1} check
 
 # devcheck: Run Infernal developer test suite (slower, but more comprehensive than 'check').
 #
 devcheck:
+	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make devcheck', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} devcheck
 
 # pdf: compile the User Guides.

README

 Infernal - inference of RNA secondary structure alignments
 http://eddylab.org/infernal/
 
-Version 1.1.2; July 2016
-Copyright (C) 2016 Howard Hughes Medical Institute.
+Version 1.1.3; Nov 2019
+Copyright (C) 2019 Howard Hughes Medical Institute.
 ------------------------------------------------------------------
 
 Infernal is an implementation of covariance models (CMs), which are

RELEASE-1.1.3.md

+# Infernal 1.1.3 release notes (Nov 2019)
+
+### Infernal 1.1.3 is the third update release for Infernal 1.1.
+
+## Notable changes from 1.1.2:
+
+ * We improved how we calculate our default sequence weights (Henikoff
+   position-based weights), especially on deep alignments of 10-100K+
+   sequences. Now we calculate PB weights only on consensus columns,
+   not all columns. This avoids some cases of artifactually extreme
+   weights on very gappy alignments. Because of these changes, CMs and
+   profile HMMs built with version 1.1.3 give slightly different
+   scores compared to previous Infernal versions.
+
+ * cmpress and cmscan now work for non-calibrated models with zero
+   basepairs. Previously, to use cmpress and cmscan with a CM
+   database, all CMs in that database had to have been calibrated with
+   cmcalibrate, even those with zero basepairs. cmcalibrate determines
+   parameters for E-value statistics of CM hit results in cmsearch and
+   cmscan. Since HMM algorithms and not CM algorithms are used by
+   default in cmscan for models with zero basepairs, calibration is
+   not necessary. Calibration is still required prior to running
+   cmpress and cmscan with models with 1 or more basepairs. 
+
+ * New cmbuild option --emaxseq for allowing effective number of
+   sequences to exceed number of sequences in the alignment.
+
+ * The Easel and HMMER3 libraries which are included with Infernal have
+   undergone numerous bug fixes and improvements.
+
+## Bug fixes:
+
+ * Fixes bugs #i45 and #i46, which caused model boundaries in
+   cmsearch/cmscan output alignments to be incorrect in rare cases
+   involving EL (local end) and truncated alignments.
+
+ * Fixes bug #i47, which prevented the cmbuild --p7ml option from
+   working correctly.
+
+ * Fixes bug #i48, which eliminates a possible ambiguity in the
+   sorting function used to sort hits for cmsearch/cmscan.
+
+ * Fixes bug #i49, which caused some potentially high scoring hits to
+   be missed cmsearch/cmscan was run in 'hmmonly' mode (default model
+   if model has 0 basepairs) when two hits are adjacent to one
+   another in the sequence.
+
+## Other smaller changes:
+
+ * New cmbuild options --occfile, --cp9occfile, and --fp7occfile for
+   outputting expected occupancy of each CM, CP9 HMM and FP7 HMM
+   states to a file.
+ 
+ * New cmsearch/cmscan option --olonepass to restrict CM analysis to
+   pipeline stage with the best HMM score for any hits that overlap.
+
+ * New cmsearch/cmscan option --noiter to turn off iterative
+   tightening of bands during CM analysis at end of pipeline.
+
+ * Our fasta format parser now detects aligned FASTA format (.afa
+   files) more robustly, and will not attempt to read a .afa file as
+   an unaligned sequence file. [iss#153]
+
+ * Our `make check` tests depend on Python >= 3.5. Added checks in
+   `./configure` and `make` to fail gracefully if python3 isn't available.
+
+ * `./configure` now always calls `AC_PROG_CC_STDC` to add compiler flags
+   for C99 (even with icc).
+
+________________________________________________________________
+
+For even more information, you can peruse the
+[git log for our develop branch](https://github.com/EddyRivasLab/infernal/commits/develop).
+

RELEASE-NOTES

-Infernal 1.1.2 release notes
-http://eddylab.org/infernal/
-EPN, Fri Jul  1 16:28:48 2016
-________________________________________________________________
-
-Infernal 1.1.2 is the second update release for Infernal 1.1.
-
-Notable changes from 1.1.1:
-
- - cmscan is significantly improved, and can now be used for genome
-   annotation; enhancements include:
-   o speed improvements due to storage of models in memory instead of
-     rereading from disk for each query sequence
-   o overlapping hits are annotated in tabular output files
-     with the --tblout <f> --fmt 2 option combination
-   o clan membership (a la Rfam) is annotated in tabular output files
-     with the --tblout <f> --fmt 2 --clanin <f> option combination.
-   o there is no longer a maximum query sequence length 
-
- - the Easel and HMMER3 libraries which are included with Infernal have
-   undergone numerous bug fixes and improvements. 
-
- - Fixed bug #i44, which caused a problem with the cmalign --mapstr
-   option if only one half of a base pair in the input alignment
-   structure was modelled by a consensus position (and the other was
-   modelled as an insert).
-
-________________________________________________________________
-For more information, see http://eddylab.org/infernal/

debian/changelog

+infernal (1.1.3-1) unstable; urgency=medium
+
+  * New upstream version
+    - Upstream accepted patch for reproducible builds
+    - autoreconf now works without respective non-applicable patch
+  * Still debian/TODO: remove code copy of hmmer
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+
+ -- Steffen Moeller <moeller@debian.org>  Sat, 30 Nov 2019 00:03:03 +0100
+
 infernal (1.1.2-2) unstable; urgency=medium
 
   * Fix homepage

debian/compat

-11

debian/control

@@ -4,9 +4,9 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libperl4-corelibs-perl
-Standards-Version: 4.1.5
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/infernal
 Vcs-Git: https://salsa.debian.org/med-team/infernal.git
 Homepage: http://eddylab.org/infernal/

debian/infernal.docs

 README
-RELEASE-NOTES
+RELEASE-*.md

debian/patches/reproducible.patch

-Description: make build reproducible
- Make Infernal build reproducible by adding support for
- SOURCE_DATE_EPOCH to the CM creation code.
-Author: Sascha Steinbiss <satta@debian.org>
-Forwarded: https://github.com/EddyRivasLab/infernal/pull/3
-Applied-Upstream: https://github.com/EddyRivasLab/infernal/commit/8cd0e3ea14e58b8bd9b60db46b73198366c87168
---- a/src/cm.c
-+++ b/src/cm.c
-@@ -2854,12 +2854,17 @@ cm_AppendComlog(CM_t *cm, int argc, char
- int
- cm_SetCtime(CM_t *cm)
- {
--  char    *s = NULL;
--  time_t   date;
--  int      status;
-+  char       *s = NULL;
-+  time_t      date;
-+  int         status;
-+  const char *sde = getenv("SOURCE_DATE_EPOCH");
- 
-   ESL_ALLOC(s, 32);
--  if ((date = time(NULL)) == -1)               { status = eslESYS; goto ERROR; }
-+  if (sde) {
-+    date = strtoul(sde, NULL, 0);
-+  } else {
-+    if ((date = time(NULL)) == -1)             { status = eslESYS; goto ERROR; }
-+  }
-   if (ctime_r(&date, s) == NULL)               { status = eslESYS; goto ERROR; }
-   if ((status = esl_strchop(s, -1)) != eslOK)  {                   goto ERROR; }
-   

debian/patches/series

 #format_security.patch
-reproducible.patch
-autoreconf.patch
+#autoreconf.patch
 spelling.patch

debian/patches/spelling.patch

@@ -2,9 +2,11 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 16 Jul 2018 07:59:38 +0200
 Description: Fix spelling
 
---- a/src/cm_modelmaker.c
-+++ b/src/cm_modelmaker.c
-@@ -1373,7 +1373,7 @@ ConsensusModelmaker(const ESL_ALPHABET *
+Index: infernal/src/cm_modelmaker.c
+===================================================================
+--- infernal.orig/src/cm_modelmaker.c
++++ infernal/src/cm_modelmaker.c
+@@ -1361,7 +1361,7 @@ ConsensusModelmaker(const ESL_ALPHABET *
     */
    esl_wuss_nopseudo(ss_cons, ss_cons); /* remove pknots in place */
    ESL_ALLOC(ct, (clen+1) * sizeof(int));
@@ -13,8 +15,10 @@ Description: Fix spelling
  
    /* 2. Construct a guide tree. 
     *    This codes is borrowed from HandModelmaker(), where it
---- a/documentation/manpages/cmalign.man
-+++ b/documentation/manpages/cmalign.man
+Index: infernal/documentation/manpages/cmalign.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmalign.man
++++ infernal/documentation/manpages/cmalign.man
 @@ -309,7 +309,7 @@ only cells within the bands need be allo
  
  Importantly, HMM banding sacrifices the guarantee of determining the
@@ -33,8 +37,10 @@ Description: Fix spelling
  .I <f> 
  to the output alignment. A similar option to this one was called
  .B --withstr 
---- a/documentation/manpages/cmcalibrate.man
-+++ b/documentation/manpages/cmcalibrate.man
+Index: infernal/documentation/manpages/cmcalibrate.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmcalibrate.man
++++ infernal/documentation/manpages/cmcalibrate.man
 @@ -51,7 +51,7 @@ Interface) can be also be used for paral
  .B --mpi 
  option if Infernal was built with MPI enabled, but using more than 161
@@ -44,9 +50,11 @@ Description: Fix spelling
  guide for more information.
  
  .PP
---- a/hmmer/src/p7_builder.c
-+++ b/hmmer/src/p7_builder.c
-@@ -504,7 +504,7 @@ p7_Builder(P7_BUILDER *bld, ESL_MSA *msa
+Index: infernal/hmmer/src/p7_builder.c
+===================================================================
+--- infernal.orig/hmmer/src/p7_builder.c
++++ infernal/hmmer/src/p7_builder.c
+@@ -481,7 +481,7 @@ p7_Builder(P7_BUILDER *bld, ESL_MSA *msa
   *            
   * Args:      bld       - build configuration
   *            sq        - query sequence
@@ -55,19 +63,23 @@ Description: Fix spelling
   *            opt_hmm   - optRETURN: new HMM
   *            opt_gm    - optRETURN: profile corresponding to <hmm>
   *            opt_om    - optRETURN: optimized profile corresponding to <gm>
---- a/documentation/manpages/cmscan.man
-+++ b/documentation/manpages/cmscan.man
+Index: infernal/documentation/manpages/cmscan.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmscan.man
++++ infernal/documentation/manpages/cmscan.man
 @@ -746,7 +746,7 @@ option.
  
  .TP
- .BI --oskip " <f>"
+ .B --oskip
 -Omit any hit h from the tabular output file that satisifies the
 +Omit any hit h from the tabular output file that satisfies the
  following: another hit h2 overlaps with h and the E-value of h2 is
  lower than that of h. Hit h will not appear in the tabular output
  file, although it will still exist in the standard output. 
---- a/documentation/manpages/cmstat.man
-+++ b/documentation/manpages/cmstat.man
+Index: infernal/documentation/manpages/cmstat.man
+===================================================================
+--- infernal.orig/documentation/manpages/cmstat.man
++++ infernal/documentation/manpages/cmstat.man
 @@ -115,7 +115,7 @@ include Rfam GA, TC, and/or NC bit score
  and/or
  .B --cut_nc 

debian/rules

@@ -15,6 +15,7 @@ override_dh_auto_clean:
 	-cd documentation/userguide && if [ -r Makefile ]; then make distclean; fi
 	-cd easel/documentation && if [ -r Makefile ]; then make distclean; fi
 	dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
+	rm -f testsuite/i49.tbl
 
 override_dh_compress :
 	dh_compress -X.pdf