[med-svn] [Git][med-team/baitfisher][upstream] New upstream version 1.2.7+git20190123.241d060+dfsg

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / baitfisher


Commits:
aea05c6b by Nilesh Patra at 2020-08-17T19:53:06+05:30
New upstream version 1.2.7+git20190123.241d060+dfsg
- - - - -


4 changed files:

- CBlastParser.h
- Documentation/BaitFisher-BaitFilter-Manual.tex
- global-types-and-parameters.cpp
- range_functions.h


Changes:

=====================================
CBlastParser.h
=====================================
@@ -575,7 +575,7 @@ class CBlast_parser
       line.removeSpacesFront();
       line.removeSpacesBack();
       
-      if (!line.empty() && line[0] != '#') // if not a comment - allows to read the -m 9 in addition to the -m 8 output format
+      if (!line.empty() && line[0] != '#') // if not a comment - allows us to read the -m 9 in addition to the -m 8 output format
       {
 	CBlastHit* p = new CBlastHit(line, counter);
 


=====================================
Documentation/BaitFisher-BaitFilter-Manual.tex
=====================================
@@ -1515,7 +1515,7 @@ number of baits as the optimality criterion. As above, the
 console-output is redirected to two files.
 
 \item With BaitFilter version 1.0.6 a new filter mode has been introduced.
-This mode allows to keep not only one but multiple bait regions per feature, or alignment, if the
+This mode allows you to keep not only one but multiple bait regions per feature, or alignment, if the
 length of the feature or alignment is long enough so that two or more bait regions can be situated
 in the alignment with a minimum distance.
 


=====================================
global-types-and-parameters.cpp
=====================================
@@ -237,7 +237,7 @@ void read_and_init_parameters(int argc, char** argv, ostream &logerr)
 
     ValueArg<string> blast_extra_commandline_Arg("", "blast-extra-commandline",
        "When invoking the blast command, extra command line parameters can be passed to the blast program with the aid of this option. As an example, "
-       "this option allows to specify the number of threads the blast program should use. Example: --blast-extra-commandline \"-num_threads 20\" sets the number of threads to 20. ",
+       "this option allows you to specify the number of threads the blast program should use. Example: --blast-extra-commandline \"-num_threads 20\" sets the number of threads to 20. ",
        false, "", "string");
     cmd.add( blast_extra_commandline_Arg );
 
@@ -637,7 +637,7 @@ void print_parameters(FILE *of, const char *s)
   }
   else if (global_mode == 'B')
   {
-    fprintf(of, "%sFilter mode:                                      Blast filter: Remove all bait regions from output that belong to the FEATUE in which one bait has at least two good hits to the reference genome.\n", s);
+    fprintf(of, "%sFilter mode:                                      Blast filter: Remove all bait regions from output that belong to the FEATURE in which one bait has at least two good hits to the reference genome.\n", s);
   }
   else if (global_mode == 'x')
   {
@@ -765,7 +765,7 @@ void print_parameters(ostream &os, const char *s)
   }
   else if (global_mode == 'B')
   {
-    os << s << "Filter mode:                                      Blast filter: Remove all bait regions from output that belong to the FEATUE in which one bait has at least two good hits to the reference genome.\n";
+    os << s << "Filter mode:                                      Blast filter: Remove all bait regions from output that belong to the FEATURE in which one bait has at least two good hits to the reference genome.\n";
   }
   else if (global_mode == 'x')
   {


=====================================
range_functions.h
=====================================
@@ -921,7 +921,7 @@ class CRangeList
   }
 
 
-  // coverage_len allows to specify a range - double check that feature.
+  // coverage_len allows us to specify a range - double check that feature.
   double coverage_rel(Crange bds)
   {
     CRangeList rl_tmp(*this);



View it on GitLab: https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70

-- 
View it on GitLab: https://salsa.debian.org/med-team/baitfisher/-/commit/aea05c6b4cd147d418dec664083e7999bde96f70
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