[med-svn] [Git][med-team/infernal][master] 2 commits: Fix spelling

Mon Jul 16 11:31:18 BST 2018

Andreas Tille pushed to branch master at Debian Med / infernal


Commits:
421b9827 by Andreas Tille at 2018-07-16T12:20:19+02:00
Fix spelling

- - - - -
3cc895af by Andreas Tille at 2018-07-16T12:30:40+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/spelling.patch


Changes:

=====================================
debian/changelog
=====================================

--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-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 at debian.org>  Wed, 18 Jan 2017 12:56:58 +0100
+ -- Andreas Tille <tille at debian.org>  Mon, 16 Jul 2018 12:20:32 +0200
 
 infernal (1.1.2-1) unstable; urgency=medium
 


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 #format_security.patch
 reproducible.patch
 autoreconf.patch
+spelling.patch


=====================================
debian/patches/spelling.patch
=====================================
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,79 @@
+Author: Andreas Tille <tille at 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.



View it on GitLab: https://salsa.debian.org/med-team/infernal/compare/3fce8ef53b60465a9b9b2ee6e1266d2ba1fe548d...3cc895af4edfab54d50750ba8f7cf8970f63e894

-- 
View it on GitLab: https://salsa.debian.org/med-team/infernal/compare/3fce8ef53b60465a9b9b2ee6e1266d2ba1fe548d...3cc895af4edfab54d50750ba8f7cf8970f63e894
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