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 <[email protected]> Wed, 18 Jan 2017 12:56:58 +0100 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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