...
 
Commits (2)
infernal (1.1.2-2) UNRELEASED; urgency=medium
infernal (1.1.2-2) unstable; urgency=medium
* Fix homepage
* Add debian/TODO: remove code copy of hmmer
......@@ -9,8 +9,9 @@ infernal (1.1.2-2) UNRELEASED; urgency=medium
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* Fix configure.ac to enable autoreconf
* Fix spelling
-- Andreas Tille <tille@debian.org> Wed, 18 Jan 2017 12:56:58 +0100
-- Andreas Tille <tille@debian.org> Mon, 16 Jul 2018 12:20:32 +0200
infernal (1.1.2-1) unstable; urgency=medium
......
#format_security.patch
reproducible.patch
autoreconf.patch
spelling.patch
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 *
*/
esl_wuss_nopseudo(ss_cons, ss_cons); /* remove pknots in place */
ESL_ALLOC(ct, (clen+1) * sizeof(int));
- if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsisent in ConsensusModelMaker().");
+ if ((status = esl_wuss2ct(ss_cons, clen, ct)) != eslOK) ESL_FAIL(status, errbuf, "Consensus string is inconsistent in ConsensusModelMaker().");
/* 2. Construct a guide tree.
* This codes is borrowed from HandModelmaker(), where it
--- a/documentation/manpages/cmalign.man
+++ b/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
optimally accurarte or optimal alignment, which will be missed if it
-lies outside the bands. The tau paramater is the amount of probability
+lies outside the bands. The tau parameter is the amount of probability
mass considered negligible during HMM band calculation; lower values
of tau yield greater speedups but also a greater chance of missing the
optimal alignment. The default tau is 1E-7, determined empirically as
@@ -500,7 +500,7 @@ in previous versions of
.B --mapstr
Must be used in combination with
.BI --mapali " <f>".
-Propogate structural information for any pseudoknots that exist in
+Propagate structural information for any pseudoknots that exist in
.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
@@ -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
processors is not recommended because increasing past 161 won't
-accelerate the calibration. See the Installation seciton of the user
+accelerate the calibration. See the Installation section of the user
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
*
* Args: bld - build configuration
* sq - query sequence
- * bg - null model (needed to paramaterize insert emission probs)
+ * bg - null model (needed to parameterize insert emission probs)
* 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
@@ -746,7 +746,7 @@ option.
.TP
.BI --oskip " <f>"
-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
@@ -115,7 +115,7 @@ include Rfam GA, TC, and/or NC bit score
and/or
.B --cut_nc
options can be used to display E-values that correspond to the bit
-score thresholds. Seperate bit scores or E-values will be displayed
+score thresholds. Separate bit scores or E-values will be displayed
for each of the four possible CM search algorithm and model
configuration pairs: local Inside, local CYK, glocal Inside and glocal
CYK.