[med-svn] [mothur] 05/06: Refresh patches
Tomasz Buchert
tomasz at moszumanska.debian.org
Sun Feb 26 15:29:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
tomasz pushed a commit to branch master
in repository mothur.
commit 982fe226b78fc007dfceb02409130b172d7edce4
Author: Tomasz Buchert <tomasz at debian.org>
Date: Sun Feb 26 15:55:59 2017 +0100
Refresh patches
---
...-flags.patch => 0001-Add-hardening-flags.patch} | 0
.../0002-Update-version-numbers-everywhere.patch | 77 ++++++
...0003-Fix-VERSION-variable-in-the-makefile.patch | 21 --
...mmand.patch => 0003-Fix-catchall-command.patch} | 25 +-
debian/patches/series | 7 +-
debian/patches/spelling.patch | 300 ---------------------
6 files changed, 92 insertions(+), 338 deletions(-)
diff --git a/debian/patches/0002-Add-hardening-flags.patch b/debian/patches/0001-Add-hardening-flags.patch
similarity index 100%
rename from debian/patches/0002-Add-hardening-flags.patch
rename to debian/patches/0001-Add-hardening-flags.patch
diff --git a/debian/patches/0002-Update-version-numbers-everywhere.patch b/debian/patches/0002-Update-version-numbers-everywhere.patch
new file mode 100644
index 0000000..e9ff0d8
--- /dev/null
+++ b/debian/patches/0002-Update-version-numbers-everywhere.patch
@@ -0,0 +1,77 @@
+From: Tomasz Buchert <tomasz at debian.org>
+Date: Sun, 26 Feb 2017 15:47:54 +0100
+Subject: Update version numbers everywhere.
+
+The upstream regularly forgets to update version numbers in the source files.
+---
+ Makefile | 2 +-
+ Mothur.xcodeproj/project.pbxproj | 8 ++++----
+ makefile-internal | 2 +-
+ 3 files changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index a805276..249feea 100644
+--- a/Makefile
++++ b/Makefile
+@@ -16,7 +16,7 @@ BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
+ BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
+ MOTHUR_FILES="\"Enter_your_default_path_here\""
+ RELEASE_DATE = "\"2/2/2017\""
+-VERSION = "\"1.39.1\""
++VERSION = "\"1.39.3\""
+
+ ifeq ($(strip $(64BIT_VERSION)),yes)
+ CXXFLAGS += -DBIT_VERSION
+diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
+index 612d786..1cbdcb5 100644
+--- a/Mothur.xcodeproj/project.pbxproj
++++ b/Mothur.xcodeproj/project.pbxproj
+@@ -3384,7 +3384,7 @@
+ GCC_MODEL_TUNING = G5;
+ GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+- "VERSION=\"\\\"1.39.2\\\"\"",
++ "VERSION=\"\\\"1.39.3\\\"\"",
+ "RELEASE_DATE=\"\\\"2/16/2017\\\"\"",
+ "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+ );
+@@ -3419,7 +3419,7 @@
+ GCC_MODEL_TUNING = G5;
+ GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+- "VERSION=\"\\\"1.39.2\\\"\"",
++ "VERSION=\"\\\"1.39.3\\\"\"",
+ "RELEASE_DATE=\"\\\"2/16/2017\\\"\"",
+ "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+ );
+@@ -3455,7 +3455,7 @@
+ GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+ "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+- "VERSION=\"\\\"1.39.1\\\"\"",
++ "VERSION=\"\\\"1.39.3\\\"\"",
+ "RELEASE_DATE=\"\\\"2/2/2017\\\"\"",
+ );
+ GCC_VERSION = "";
+@@ -3505,7 +3505,7 @@
+ GCC_MODEL_TUNING = "";
+ GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_PREPROCESSOR_DEFINITIONS = (
+- "VERSION=\"\\\"1.39.2\\\"\"",
++ "VERSION=\"\\\"1.39.3\\\"\"",
+ "RELEASE_DATE=\"\\\"2/16/2017\\\"\"",
+ "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
+ );
+diff --git a/makefile-internal b/makefile-internal
+index 3e017db..85a4d64 100644
+--- a/makefile-internal
++++ b/makefile-internal
+@@ -2,7 +2,7 @@
+ USEREADLINE ?= no
+ USEBOOST ?= no
+ RELEASE_DATE = "\"2/7/2017\""
+-VERSION = "\"1.39.1\""
++VERSION = "\"1.39.3\""
+
+ # Optimize to level 3:
+ CXXFLAGS += -O3
diff --git a/debian/patches/0003-Fix-VERSION-variable-in-the-makefile.patch b/debian/patches/0003-Fix-VERSION-variable-in-the-makefile.patch
deleted file mode 100644
index a81a13e..0000000
--- a/debian/patches/0003-Fix-VERSION-variable-in-the-makefile.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-From: Tomasz Buchert <tomasz at debian.org>
-Date: Sat, 30 Jul 2016 01:49:56 +0200
-Subject: Fix VERSION variable in the makefile.
-
----
- source/makefile | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/makefile b/source/makefile
-index fe1d1d4..bedd70b 100644
---- a/source/makefile
-+++ b/source/makefile
-@@ -16,7 +16,7 @@ MOTHUR_FILES="\"Enter_your_default_path_here\""
- BOOST_INCLUDE_DIR="/usr/local/include/"
- BOOST_LIBRARY_DIR="/usr/local/lib/"
- RELEASE_DATE = "\"4/22/2015\""
--VERSION = "\"1.35.1\""
-+VERSION = "\"1.38.0\""
- FORTAN_COMPILER = gfortran
- FORTRAN_FLAGS =
-
diff --git a/debian/patches/0001-Fix-catchall-command.patch b/debian/patches/0003-Fix-catchall-command.patch
similarity index 67%
rename from debian/patches/0001-Fix-catchall-command.patch
rename to debian/patches/0003-Fix-catchall-command.patch
index 9da2780..db63df0 100644
--- a/debian/patches/0001-Fix-catchall-command.patch
+++ b/debian/patches/0003-Fix-catchall-command.patch
@@ -1,19 +1,16 @@
From: Tomasz Buchert <tomasz at debian.org>
-Date: Fri, 4 Sep 2015 00:04:02 +0200
+Date: Sun, 26 Feb 2017 15:52:43 +0100
Subject: Fix catchall command
This removes a workaround that is better fixed in Catchall than in
-Mothur, so I did that (packaged in bio-linux-catchall just now as I
-don't have the source compiling yet.)
-
-This patch is a refreshed version of a patch without authorship
-information.
+Mothur (packaged in bio-linux-catchall just now as I don't have the
+source compiling yet.)
---
- source/commands/catchallcommand.cpp | 6 ++++++
- 1 file changed, 6 insertions(+)
+ source/commands/catchallcommand.cpp | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/source/commands/catchallcommand.cpp b/source/commands/catchallcommand.cpp
-index 74f02e1..8d22971 100644
+index 4d65bd6..4ac04d4 100644
--- a/source/commands/catchallcommand.cpp
+++ b/source/commands/catchallcommand.cpp
@@ -199,6 +199,7 @@ int CatchAllCommand::execute() {
@@ -22,17 +19,19 @@ index 74f02e1..8d22971 100644
+ /* TB for Bio-Linux: Don't need this...
//get location of catchall
- path = m->argv;
- path = path.substr(0, (path.find_last_of("othur")-5));
-@@ -257,6 +258,11 @@ int CatchAllCommand::execute() {
+ path = m->mothurProgramPath;
+ //path = path.substr(0, (path.find_last_of("othur")-5));
+@@ -257,7 +258,12 @@ int CatchAllCommand::execute() {
//prepare full output directory
outputDir = m->getFullPathName(outputDir);
+-
+ */
+
+ /* TB for Bio-Linux: We just need this, assuming catchall is properly wrapped to avoid
+ * the bug described above - see the bio-linux-catchall package */
+ string catchAllCommandExe = "catchall ";
-
++
if (m->debug) { m->mothurOut("[DEBUG]: catchall location = " + catchAllCommandExe + "\n[DEBUG]: outputDir = " + outputDir + "\n"); }
+ vector<string> inputFileNames;
diff --git a/debian/patches/series b/debian/patches/series
index d3e4b77..efa24cf 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-0001-Fix-catchall-command.patch
-0002-Add-hardening-flags.patch
-0003-Fix-VERSION-variable-in-the-makefile.patch
-spelling.patch
+0001-Add-hardening-flags.patch
+0002-Update-version-numbers-everywhere.patch
+0003-Fix-catchall-command.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 8f50c64..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,300 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 10 Dec 2016 06:35:47 +0100
-Description: Fix spelling
-
---- a/source/commandfactory.cpp
-+++ b/source/commandfactory.cpp
-@@ -1018,7 +1018,7 @@ void CommandFactory::printCommandsCatego
- }
-
- for (itCat = categories.begin(); itCat != categories.end(); itCat++) {
-- out << itCat->first << " commmands include: " << itCat->second << endl;
-+ out << itCat->first << " commands include: " << itCat->second << endl;
- }
-
- }
---- a/source/commands/clusterfragmentscommand.cpp
-+++ b/source/commands/clusterfragmentscommand.cpp
-@@ -334,7 +334,7 @@ bool ClusterFragmentsCommand::isFragment
-
- //find number of acceptable differences for this sequence fragment
- int totalDiffs = 0;
-- if (diffs == 0) { //you didnt set diffs you want a percentage
-+ if (diffs == 0) { //you didn't set diffs you want a percentage
- totalDiffs = floor((seq2.length() * (percent / 100.0)));
- }else if (percent == 0) { //you didn't set percent you want diffs
- totalDiffs = diffs;
---- a/source/commands/getgroupscommand.cpp
-+++ b/source/commands/getgroupscommand.cpp
-@@ -46,7 +46,7 @@ vector<string> GetGroupsCommand::setPara
- string GetGroupsCommand::getHelpString(){
- try {
- string helpString = "";
-- helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design, phylip, column or shared file.\n";
-+ helpString += "The get.groups command selects sequences from a specific group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design, phylip, column or shared file.\n";
- helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n";
- helpString += "The get.groups command parameters are accnos, fasta, name, group, count, list, taxonomy, shared, design, phylip, column and groups. The group or count parameter is required, unless you have a current group or count file, or are using a shared file.\n";
- helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
---- a/source/commands/getotuscommand.cpp
-+++ b/source/commands/getotuscommand.cpp
-@@ -37,7 +37,7 @@ vector<string> GetOtusCommand::setParame
- string GetOtusCommand::getHelpString(){
- try {
- string helpString = "";
-- helpString += "The get.otus command selects otus containing sequences from a specfic group or set of groups.\n";
-+ helpString += "The get.otus command selects otus containing sequences from a specific group or set of groups.\n";
- helpString += "It outputs a new list file containing the otus containing sequences from in the those specified groups.\n";
- helpString += "The get.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n";
- helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
---- a/source/commands/indicatorcommand.cpp
-+++ b/source/commands/indicatorcommand.cpp
-@@ -762,7 +762,7 @@ vector<float> IndicatorCommand::getValue
- vector<int> temp; temp.push_back(j); temp.push_back(k);
- it = groupingsMap.find(temp);
-
-- if (it == groupingsMap.end()) { //this one didnt get moved
-+ if (it == groupingsMap.end()) { //this one didn't get moved
- totalAbund += groupings[j][k]->getAbundance(i);
- if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
- }else {
-@@ -838,7 +838,7 @@ vector<float> IndicatorCommand::getValue
- vector<int> temp; temp.push_back(j); temp.push_back(k);
- it = groupingsMap.find(temp);
-
-- if (it == groupingsMap.end()) { //this one didnt get moved
-+ if (it == groupingsMap.end()) { //this one didn't get moved
- totalAbund += groupings[j][k]->getAbundance(i);
- if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
- }else {
---- a/source/commands/indicatorcommand.h
-+++ b/source/commands/indicatorcommand.h
-@@ -147,7 +147,7 @@ static DWORD WINAPI MyIndicatorThreadFun
- vector<int> temp; temp.push_back(j); temp.push_back(k);
- it = randomGroupings.find(temp);
-
-- if (it == randomGroupings.end()) { //this one didnt get moved
-+ if (it == randomGroupings.end()) { //this one didn't get moved
- totalAbund += pDataArray->groupings[j][k]->getAbundance(i);
- if (pDataArray->groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
- }else {
---- a/source/commands/mergetaxsummarycommand.cpp
-+++ b/source/commands/mergetaxsummarycommand.cpp
-@@ -213,7 +213,7 @@ int MergeTaxSummaryCommand::execute(){
- else {
- map<int, int>::iterator itParent = levelToCurrentNode.find(level-1);
- int parent = 0;
-- if (itParent == levelToCurrentNode.end()) { m->mothurOut("[ERROR]: situation I didnt expect.\n"); }
-+ if (itParent == levelToCurrentNode.end()) { m->mothurOut("[ERROR]: situation I didn't expect.\n"); }
- else { parent = itParent->second; }
-
- levelToCurrentNode[level] = addTaxToTree(tree, level, parent, tax, total, groupCounts);
---- a/source/commands/removegroupscommand.cpp
-+++ b/source/commands/removegroupscommand.cpp
-@@ -46,7 +46,7 @@ vector<string> RemoveGroupsCommand::setP
- string RemoveGroupsCommand::getHelpString(){
- try {
- string helpString = "";
-- helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design, phylip, column or sharedfile.\n";
-+ helpString += "The remove.groups command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design, phylip, column or sharedfile.\n";
- helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n";
- helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design, phylip, column and groups. The group or count parameter is required, unless you have a current group or count file or are using a sharedfile.\n";
- helpString += "You must also provide an accnos containing the list of groups to remove or set the groups parameter to the groups you wish to remove.\n";
---- a/source/commands/removeotuscommand.cpp
-+++ b/source/commands/removeotuscommand.cpp
-@@ -36,7 +36,7 @@ vector<string> RemoveOtusCommand::setPar
- string RemoveOtusCommand::getHelpString(){
- try {
- string helpString = "";
-- helpString += "The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n";
-+ helpString += "The remove.otus command removes otus containing sequences from a specific group or set of groups.\n";
- helpString += "It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n";
- helpString += "The remove.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n";
- helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
---- a/source/uchime_src/help.h
-+++ b/source/uchime_src/help.h
-@@ -39,7 +39,7 @@
- " that support or contradict a chimeric model.\n"
- "\n"
- "--minh h\n"
--" Mininum score to report chimera. Default 0.3. Values from 0.1\n"
-+" Minimum score to report chimera. Default 0.3. Values from 0.1\n"
- " to 5 might be reasonable. Lower values increase sensitivity\n"
- " but may report more false positives. If you decrease --xn,\n"
- " you may need to increase --minh, and vice versa.\n"
---- a/source/commands/chimerauchimecommand.cpp
-+++ b/source/commands/chimerauchimecommand.cpp
-@@ -72,7 +72,7 @@ string ChimeraUchimeCommand::getHelpStri
- helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
- helpString += "The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).\n";
- helpString += "The chimealns parameter allows you to indicate you would like a file containing multiple alignments of query sequences to parents in human readable format. Alignments show columns with differences that support or contradict a chimeric model.\n";
-- helpString += "The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
-+ helpString += "The minh parameter - minimum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
- helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease minh, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
- helpString += "The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.\n";
- helpString += "The dn parameter - pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.\n";
---- a/source/commands/chimeravsearchcommand.cpp
-+++ b/source/commands/chimeravsearchcommand.cpp
-@@ -59,7 +59,7 @@ string ChimeraVsearchCommand::getHelpStr
- helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
- helpString += "The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).\n";
- helpString += "The uchimealns parameter allows you to indicate you would like a file containing multiple alignments of query sequences to parents in human readable format. Alignments show columns with differences that support or contradict a chimeric model.\n";
-- helpString += "The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
-+ helpString += "The minh parameter - minimum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
- helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease minh, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
- helpString += "The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.\n";
- helpString += "The dn parameter - pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.\n";
---- a/source/commands/classifyotucommand.cpp
-+++ b/source/commands/classifyotucommand.cpp
-@@ -63,7 +63,7 @@ string ClassifyOtuCommand::getHelpString
- helpString += "The printlevel parameter allows you to specify taxlevel of your summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level. If you select a level greater than the level your sequences classify to, mothur will print to the level your max level. \n";
- helpString += "The cutoff parameter allows you to specify a consensus confidence threshold for your otu taxonomy output. The default is 51, meaning 51%. Cutoff cannot be below 51.\n";
- helpString += "The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.\n";
-- helpString += "The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted. Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus. This feature is similar to adjusting the cutoff in classify.seqs. Default=0.\n";
-+ helpString += "The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted. Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the consensus. This feature is similar to adjusting the cutoff in classify.seqs. Default=0.\n";
- helpString += "The classify.otu command should be in the following format: classify.otu(taxonomy=yourTaxonomyFile, list=yourListFile, name=yourNamesFile, label=yourLabels).\n";
- helpString += "Example classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, label=0.10).\n";
- helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
---- a/source/commands/classifyotucommand.h
-+++ b/source/commands/classifyotucommand.h
-@@ -30,7 +30,7 @@ public:
- string getHelpString();
- string getOutputPattern(string);
- string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
-- string getDescription() { return "find the concensus taxonomy for each OTU"; }
-+ string getDescription() { return "find the consensus taxonomy for each OTU"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
---- a/source/commands/classifytreecommand.cpp
-+++ b/source/commands/classifytreecommand.cpp
-@@ -38,10 +38,10 @@ string ClassifyTreeCommand::getHelpStrin
- try {
- string helpString = "";
- helpString += "The classify.tree command reads a tree and taxonomy file and output the consensus taxonomy for each node on the tree. \n";
-- helpString += "If you provide a group file, the concensus for each group will also be provided. \n";
-+ helpString += "If you provide a group file, the consensus for each group will also be provided. \n";
- helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n";
- helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
-- helpString += "The summary file lists the concensus taxonomy for the descendants of each node.\n";
-+ helpString += "The summary file lists the consensus taxonomy for the descendants of each node.\n";
- helpString += "The classify.tree command parameters are tree, group, name, count and taxonomy. The tree and taxonomy files are required.\n";
- helpString += "The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy. The default is 51, meaning 51%. Cutoff cannot be below 51.\n";
- helpString += "The output parameter allows you to specify whether you want the tree node number displayed on the tree, or the taxonomy displayed. Default=node. Options are node or taxon.\n";
-@@ -252,7 +252,7 @@ int ClassifyTreeCommand::execute(){
- m->readTax(taxonomyfile, taxMap, true);
-
- /***************************************************/
-- // get concensus taxonomies //
-+ // get consensus taxonomies //
- /***************************************************/
- getClassifications(outputTree);
- delete outputTree; delete tmap;
-@@ -268,7 +268,7 @@ int ClassifyTreeCommand::execute(){
- }
- }
-
-- m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the concensus taxonomies."); m->mothurOutEndLine();
-+ m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the consensus taxonomies."); m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
-@@ -282,9 +282,9 @@ int ClassifyTreeCommand::execute(){
- }
- }
- //**********************************************************************************************************************
--//traverse tree finding concensus taxonomy at each node
-+//traverse tree finding consensus taxonomy at each node
- //label node with a number to relate to output summary file
--//report all concensus taxonomies to file
-+//report all consensus taxonomies to file
- int ClassifyTreeCommand::getClassifications(Tree*& T){
- try {
-
---- a/source/commands/getcoremicrobiomecommand.cpp
-+++ b/source/commands/getcoremicrobiomecommand.cpp
-@@ -42,7 +42,7 @@ string GetCoreMicroBiomeCommand::getHelp
- helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
- helpString += "The output parameter is used to specify whether you would like the fraction of OTU's or OTU count outputted. Options are fraction or count. Default=fraction.\n";
- helpString += "The abundance parameter allows you to specify an abundance you would like the OTU names outputted for. Values 1 to 100, will be treated as the percentage. For example relabund=0.01 can be set with abundance=1 or abundance=0.01. For abundance values < 1 percent, abundance=0.001 will specify OTUs with relative abundance of 0.001.\n";
-- helpString += "The samples parameter allows you to specify the minimum number of samples you would like the OTU names outputted for. Must be an interger between 1 and number of samples in your file.\n";
-+ helpString += "The samples parameter allows you to specify the minimum number of samples you would like the OTU names outputted for. Must be an integer between 1 and number of samples in your file.\n";
- helpString += "The new command should be in the following format: get.coremicrobiome(shared=yourSharedFile)\n";
- helpString += "get.coremicrobiom(shared=final.an.shared, abund=30)\n";
- return helpString;
---- a/source/commands/lefsecommand.cpp
-+++ b/source/commands/lefsecommand.cpp
-@@ -573,7 +573,7 @@ bool LefseCommand::testOTUWilcoxon(map<s
- vector< set<string> > allDiffs;
- LinearAlgebra linear;
-
-- //for each subclass comparision
-+ //for each subclass comparison
- map<string, set<string> >::iterator itB;
- for(map<string, set<string> >::iterator it=class2SubClasses.begin();it!=class2SubClasses.end();it++){
- itB = it;itB++;
---- a/source/commands/summarytaxcommand.cpp
-+++ b/source/commands/summarytaxcommand.cpp
-@@ -43,7 +43,7 @@ string SummaryTaxCommand::getHelpString(
- helpString += "The name parameter allows you to enter a name file associated with your taxonomy file. \n";
- helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
- helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
-- helpString += "The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted. Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus. This feature is similar to adjusting the cutoff in classify.seqs. Default=0.\n";
-+ helpString += "The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted. Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the consensus. This feature is similar to adjusting the cutoff in classify.seqs. Default=0.\n";
- helpString += "The output parameter allows you to specify format of your summary file. Options are simple and detail. The default is detail.\n";
- helpString += "The printlevel parameter allows you to specify taxlevel of your summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level. If you select a level greater than the level your sequences classify to, mothur will print to the level your max level. \n";
- helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";
---- a/source/commands/unifracunweightedcommand.cpp
-+++ b/source/commands/unifracunweightedcommand.cpp
-@@ -49,7 +49,7 @@ string UnifracUnweightedCommand::getHelp
- helpString += "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
- helpString += "The distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n";
- helpString += "The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n";
-- helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparision instead of the root of the entire tree.\n";
-+ helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparison instead of the root of the entire tree.\n";
- helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
- helpString += "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n";
- helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a group file.\n";
---- a/source/commands/unifracweightedcommand.cpp
-+++ b/source/commands/unifracweightedcommand.cpp
-@@ -49,7 +49,7 @@ string UnifracWeightedCommand::getHelpSt
- helpString += "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
- helpString += "The distance parameter allows you to create a distance file from the results. The default is false.\n";
- helpString += "The random parameter allows you to shut off the comparison to random trees. The default is false, meaning don't compare your trees with randomly generated trees.\n";
-- helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparision instead of the root of the entire tree.\n";
-+ helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparison instead of the root of the entire tree.\n";
- helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
- helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a group file.\n";
- helpString += "The consensus parameter allows you to indicate you would like trees built from distance matrices created with the results, as well as a consensus tree built from these trees. Default=F.\n";
---- a/source/commands/chopseqscommand.cpp
-+++ b/source/commands/chopseqscommand.cpp
-@@ -51,7 +51,7 @@ string ChopSeqsCommand::getHelpString(){
- helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
- helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
- helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
-- helpString += "The keepn parameter allows you to specify you want to keep ambigous bases, default=false.\n";
-+ helpString += "The keepn parameter allows you to specify you want to keep ambiguous bases, default=false.\n";
- helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
- helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
- helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
---- a/source/commands/setcurrentcommand.cpp
-+++ b/source/commands/setcurrentcommand.cpp
-@@ -60,7 +60,7 @@ string SetCurrentCommand::getHelpString(
- helpString += "The set.current command allows you to set the current files saved by mothur.\n";
- helpString += "The set.current command parameters are: current, clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary, file and taxonomy.\n";
- helpString += "The current parameter is used to input the output file from get.current. This function is intended to allow you to input filenames from previous instances on mothur. NOTE: If you have a current file set in the file *.current_files.summary file, and also set a value for that file type, the value set takes precedence. For example, if you run set.current(current=current_files.summary, fasta=abrecovery.fasta) and your have fasta=final.fasta in the *.current_files.s [...]
-- helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
-+ helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
- helpString += "The set.current command should be in the following format: \n";
- helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
- return helpString;
---- a/source/commands/trimseqscommand.cpp
-+++ b/source/commands/trimseqscommand.cpp
-@@ -352,7 +352,7 @@ TrimSeqsCommand::TrimSeqsCommand(string
- qThreshold=0;
- }
- if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
-- m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
-+ m->mothurOut("You didn't set any options... quitting command."); m->mothurOutEndLine();
- abort = true;
- }
-
--
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