[med-svn] [Git][med-team/libvcflib][master] fix spelling typos
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Sep 4 05:00:11 BST 2019
Michael R. Crusoe pushed to branch master at Debian Med / libvcflib
Commits:
a99be0fd by Michael R. Crusoe at 2019-09-04T03:57:23Z
fix spelling typos
- - - - -
2 changed files:
- debian/patches/series
- + debian/patches/spelling
Changes:
=====================================
debian/patches/series
=====================================
@@ -13,3 +13,4 @@ fix_installation.patch
dont_link_pthread
override_version
hardening-flags
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,145 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: lintian-inspired spelling fixes
+--- libvcflib.orig/src/abba-baba.cpp
++++ libvcflib/src/abba-baba.cpp
+@@ -47,7 +47,7 @@
+
+ cerr << "INFO: usage: abba-baba --tree 0,1,2,3 --file my.vcf --type PL" << endl;
+ cerr << endl;
+- cerr << "INFO: required: t,tree -- a zero based comma seperated list of target individuals corrisponding to VCF columns" << endl;
++ cerr << "INFO: required: t,tree -- a zero based comma separated list of target individuals corrisponding to VCF columns" << endl;
+ cerr << "INFO: required: f,file -- a properly formatted VCF. " << endl;
+ cerr << "INFO: required: y,type -- genotype likelihood format ; genotypes: GP,GL or PL; " << endl;
+ cerr << endl;
+--- libvcflib.orig/src/gl-XPEHH.cpp
++++ libvcflib/src/gl-XPEHH.cpp
+@@ -488,8 +488,8 @@
+ cerr << "INFO: gl-XPEHH --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --deltaaf 0.1 --ancestral 0 " << endl;
+ cerr << endl;
+ cerr << "INFO: required: r,region -- a genomice range to calculate gl-XPEHH on in the format : \"seqid:start-end]\" or \"seqid\" " << endl;
+- cerr << "INFO: required: t,target -- a zero base comma seperated list of target individuals corrisponding to VCF columns " << endl;
+- cerr << "INFO: required: b,background -- a zero base comma seperated list of background individuals corrisponding to VCF columns " << endl;
++ cerr << "INFO: required: t,target -- a zero base comma separated list of target individuals corrisponding to VCF columns " << endl;
++ cerr << "INFO: required: b,background -- a zero base comma separated list of background individuals corrisponding to VCF columns " << endl;
+ cerr << "INFO: required: f,file a -- proper formatted VCF. the FORMAT field MUST contain \"PL\" if option phased == 0 " << endl;
+ cerr << "INFO: optional: m,mutation -- which state is derived in vcf [0,1] default is 1 " << endl;
+ cerr << "INFO: optional: p,phased -- phasing flag [0,1] 0 = phase vcf, 1 = vcf is already phased " << endl;
+--- libvcflib.orig/src/hapLrt.cpp
++++ libvcflib/src/hapLrt.cpp
+@@ -24,7 +24,7 @@
+ cerr << endl << endl;
+ cerr << "INFO: help" << endl;
+ cerr << "INFO: description:" << endl;
+- cerr << " HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribtuion. " << endl;
++ cerr << " HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribution. " << endl;
+ cerr << " The sign denotes if the target has longer haplotypes (1) or the background (-1). " << endl << endl;
+
+ cerr << "Output : 4 columns : " << endl;
+@@ -38,8 +38,8 @@
+ cerr << "INFO: hapLRT --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --type GP --file my.vcf " << endl;
+ cerr << endl;
+
+- cerr << "INFO: required: t,target -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns " << endl;
+- cerr << "INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns " << endl;
++ cerr << "INFO: required: t,target -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns " << endl;
++ cerr << "INFO: required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns " << endl;
+ cerr << "INFO: required: f,file -- argument: a properly formatted phased VCF file " << endl;
+ cerr << "INFO: required: y,type -- argument: type of genotype likelihood: PL, GL or GP " << endl;
+ cerr << "INFO: optional: r,region -- argument: a genomice range to calculate hapLrt on in the format : \"seqid:start-end\" or \"seqid\" " << endl;
+--- libvcflib.orig/src/vcfld.cpp
++++ libvcflib/src/vcfld.cpp
+@@ -26,8 +26,8 @@
+ cerr << "INFO: LD --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf -e -d -r " << endl;
+ cerr << endl;
+
+- cerr << "INFO: required: t,target -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns " << endl;
+- cerr << "INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns " << endl;
++ cerr << "INFO: required: t,target -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns " << endl;
++ cerr << "INFO: required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns " << endl;
+ cerr << "INFO: required: f,file -- argument: a properly formatted phased VCF file " << endl;
+ cerr << "INFO: required: y,type -- argument: type of genotype likelihood: PL, GL or GP " << endl;
+ cerr << "INFO: optional: w,window -- argument: window size to average LD; default is 1000 " << endl;
+--- libvcflib.orig/src/genotypeSummary.cpp
++++ libvcflib/src/genotypeSummary.cpp
+@@ -356,7 +356,7 @@
+ }
+ }
+ else{
+- std::cerr << "FATAL: unkown genotype index" << std::endl;
++ std::cerr << "FATAL: unknown genotype index" << std::endl;
+ cerr << populationTarget->genoIndex[i] << endl;
+ cerr << var << endl;
+ exit(1);
+--- libvcflib.orig/src/permuteGPAT++.cpp
++++ libvcflib/src/permuteGPAT++.cpp
+@@ -169,7 +169,7 @@
+ }
+ }
+ else{
+- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;
++ cerr << "FATAL: could not open file: " << globalOpts.file << endl;
+ exit(1);
+ }
+
+@@ -214,7 +214,7 @@
+
+ }
+ else{
+- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;
++ cerr << "FATAL: could not open file: " << globalOpts.file << endl;
+ exit(1);
+ }
+
+--- libvcflib.orig/src/permuteGPATsmoother.cpp
++++ libvcflib/src/permuteGPATsmoother.cpp
+@@ -170,7 +170,7 @@
+ }
+ }
+ else{
+- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;
++ cerr << "FATAL: could not open file: " << globalOpts.file << endl;
+ exit(1);
+ }
+
+@@ -214,7 +214,7 @@
+ }
+ }
+ else{
+- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;
++ cerr << "FATAL: could not open file: " << globalOpts.file << endl;
+ exit(1);
+ }
+
+--- libvcflib.orig/src/permuteRegions.cpp
++++ libvcflib/src/permuteRegions.cpp
+@@ -340,7 +340,7 @@
+ }
+ }
+ else{
+- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;
++ cerr << "FATAL: could not open file: " << globalOpts.file << endl;
+ exit(1);
+ }
+
+--- libvcflib.orig/src/permuteSmooth.cpp
++++ libvcflib/src/permuteSmooth.cpp
+@@ -356,7 +356,7 @@
+ }
+ }
+ else{
+- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;
++ cerr << "FATAL: could not open file: " << globalOpts.file << endl;
+ exit(1);
+ }
+
+--- libvcflib.orig/src/plotHaps.cpp
++++ libvcflib/src/plotHaps.cpp
+@@ -281,7 +281,7 @@
+ }
+ }
+ else{
+- cerr << "FATAL: must specifiy a region" << endl;
++ cerr << "FATAL: must specify a region" << endl;
+ printHelp();
+ return 1;
+ }
View it on GitLab: https://salsa.debian.org/med-team/libvcflib/commit/a99be0fdb5ec1303d15203f44898a5716f8541d8
--
View it on GitLab: https://salsa.debian.org/med-team/libvcflib/commit/a99be0fdb5ec1303d15203f44898a5716f8541d8
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