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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