[med-svn] r8494 - trunk/packages/gmod/chado/trunk/debian/patches
olivier sallou
osallou-guest at alioth.debian.org
Wed Nov 9 14:16:25 UTC 2011
Author: osallou-guest
Date: 2011-11-09 14:16:24 +0000 (Wed, 09 Nov 2011)
New Revision: 8494
Added:
trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage
Modified:
trunk/packages/gmod/chado/trunk/debian/patches/series
Log:
fix spelling errors in man pages
Added: trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage 2011-11-09 14:16:24 UTC (rev 8494)
@@ -0,0 +1,213 @@
+Subject: Fix spelling errors
+Author: Olivier Salllou <olivier.sallou at irisa.fr>
+Description: fix spelling errors in man pages
+Last-Updated: 09/11/11
+--- a/lib/Bio/GMOD/DB/Adapter.pm
++++ b/lib/Bio/GMOD/DB/Adapter.pm
+@@ -868,7 +868,7 @@
+
+ =item Returns
+
+-On create, void. With an arguement, returns the requested file handle
++On create, void. With an argument, returns the requested file handle
+
+ =item Arguments
+
+@@ -968,7 +968,7 @@
+
+ =item Returns
+
+-See Arguements.
++See Arguments.
+
+ =item Arguments
+
+@@ -3470,7 +3470,7 @@
+ -- short identifier that can help people find an analysis they
+ -- want. for instance "tRNAscan", "cDNA", "FlyPep", "SwissProt"
+ -- it should not be assumed to be unique. for instance, there may
+--- be lots of seperate analyses done against a cDNA database.
++-- be lots of separate analyses done against a cDNA database.
+ --
+ -- program: not NULL (and programversion is NOT NULL...)
+ -- e.g. blastx, blastp, sim4, genscan
+--- a/lib/Bio/GMOD/Config2.pm
++++ b/lib/Bio/GMOD/Config2.pm
+@@ -81,7 +81,7 @@
+
+ Takes one optional argument that is the path to the root of the GMOD
+ installation. If that argument is not provided, Bio::GMOD::Config will
+-fall back to the enviroment variable GMOD_ROOT, which should be defined
++fall back to the environment variable GMOD_ROOT, which should be defined
+ for any GMOD installation.
+
+ =cut
+@@ -267,7 +267,7 @@
+
+ =head2 appendHash($tohash, $addhash, $replace)
+
+-add keys to hash without replacing existing .. prefered behavior ?
++add keys to hash without replacing existing .. preferred behavior ?
+ unless $replace is flagged
+
+ =cut
+--- a/lib/Bio/GMOD/Config.pm
++++ b/lib/Bio/GMOD/Config.pm
+@@ -41,7 +41,7 @@
+
+ Takes one optional argument that is the path to the root of the GMOD
+ installation. If that argument is not provided, Bio::GMOD::Config will
+-fall back to the enviroment variable GMOD_ROOT, which should be defined
++fall back to the environment variable GMOD_ROOT, which should be defined
+ for any GMOD installation.
+
+ =cut
+--- a/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
++++ b/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
+@@ -640,7 +640,7 @@
+ full of match: analysis types (messy names, types, etc.)
+ -- no feats written to fff in many hours !? - due to holding BAC and cytoband features
+ -- try dropping gffForwards; maybe better (gff written) but still memuse balloons
+- -- added clearFinishedObs() - no apparent help; dont see what else is holding objects here
++ -- added clearFinishedObs() - no apparent help; don't see what else is holding objects here
+ -- ok now, added min base loc to keep in oidobs, delete all before
+ runs fast - chr 3L in 10 min. instead of >2hr.
+
+@@ -775,8 +775,8 @@
+
+ if (!$type && $DEBUG && !/NULL|repeatmask/) { print STDERR "missing type: $_\n"; } ##<< repeatmasker kid objs
+ if ($type eq 'skip' || !$type) { # or what? undef? got some bad feats w/ no type??
+- ## dont keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin);
+- ##dont save arm for skip !? if changed here, cant miss below openout..
++ ## don't keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin);
++ ##don't save arm for skip !? if changed here, cant miss below openout..
+ ($l_oid,$l_fmin)= (-1,$fmin);
+ next;
+ }
+@@ -827,7 +827,7 @@
+ else {
+ ## FIXME - bad if fob not in @fobs
+ ## .. e.g. repeat region - many locs over arm, few oid's
+- ## most of these we dont want to join - too far apart; need max_max setting below to keep small ranges together?
++ ## most of these we don't want to join - too far apart; need max_max setting below to keep small ranges together?
+ # print STDERR "missed join to last $type,$name,$oid\n" if $DEBUG;
+ }
+ }
+@@ -875,7 +875,7 @@
+ if ($flushok) {
+ if ($self->hasObForwards(\@fobs, \%oidobs)) {
+ $flushok = 0;
+- $min_max= $fmin + 2000; ##smaller step so we dont miss chance to flush
++ $min_max= $fmin + 2000; ##smaller step so we don't miss chance to flush
+ }
+ warn "hasObForwards no=$flushok at $fmin $type:$name $oid\n" if ($DEBUG>1);
+ }
+@@ -908,7 +908,7 @@
+ $fob= $newob;
+ foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=();
+
+- #?? dont add here if it is simple feature; wait till know if it is parent or kid?
++ #?? don't add here if it is simple feature; wait till know if it is parent or kid?
+ # this is bad for 'gene' NOT? simple feat
+ unless( $simplefeat{$type} ) {
+ $oidobs{$oid}->{fob}= $newob;
+@@ -1157,7 +1157,7 @@
+ }
+ }
+ }
+- ## else { } # $iskid only - dont save
++ ## else { } # $iskid only - don't save
+ }
+
+ return \@cobs;
+@@ -1256,7 +1256,7 @@
+ looks like chado pg reporting instance with CDS_exons is bad for transspliced mod(mdg4)
+
+ 08may: change behavior for GenbankSubmit to offsetLocation:
+- dont return Genbank style string location, but
++ don't return Genbank style string location, but
+ adjust @loc to CDS_exons by CDS span offset;
+ See also getCDSexons and makeCompound
+
+@@ -1573,7 +1573,7 @@
+ ## for each gene model part; should add locus_tag == gene ID
+
+ # if ($gff_keepoids) { $at{$k} .= ATTR_LISTCHAR if $at{$k}; $at{$k} .= $v; }
+- next if $segmentfeats{$type}; # dont do parent for these ... ?
++ next if $segmentfeats{$type}; # don't do parent for these ... ?
+
+ $v =~ s/:.*$//;
+ $k= 'Parent';
+--- a/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
++++ b/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
+@@ -7,7 +7,7 @@
+
+ =head2 SYNOPSIS
+
+-** dgg: rewrite for line-add so dont need to suck all into mem **
++** dgg: rewrite for line-add so don't need to suck all into mem **
+
+ use SWISS::CRC64;
+
+--- a/bin/gmod_gff3_preprocessor.pl
++++ b/bin/gmod_gff3_preprocessor.pl
+@@ -23,7 +23,7 @@
+ --gfffile The file containing GFF3 (optional, can read
+ from stdin)
+ --outfile The name kernel that will be used for naming result files
+- --splitfile Split the files into more managable chunks, providing
++ --splitfile Split the files into more manageable chunks, providing
+ an argument to control splitting
+ --onlysplit Split the files and then quit (ie, don't sort)
+ --nosplit Don't split the files (ie, only sort)
+@@ -60,7 +60,7 @@
+ =head2 FASTA sequence
+
+ If the GFF3 file contains FASTA sequence at the end, the sequence
+-will be placed in a separate file with the extention '.fasta'. This
++will be placed in a separate file with the extension '.fasta'. This
+ fasta file can be loaded separately after the split and/or sorted
+ GFF3 files are loaded, using the command:
+
+--- a/bin/gmod_make_gff_from_dbxref.pl
++++ b/bin/gmod_make_gff_from_dbxref.pl
+@@ -21,7 +21,7 @@
+
+ =head1 DESCRIPTION
+
+-This tool takes a list of tab seperated db identifiers and accessions on
++This tool takes a list of tab separated db identifiers and accessions on
+ the command line (like gmod_extract_dbxref_from_gff.pl would produce)
+ along with a directory containing fasta files and creates a GFF file.
+ The script tries several options for identifying the accession in the
+--- a/bin/gmod_materialized_view_tool.pl
++++ b/bin/gmod_materialized_view_tool.pl
+@@ -58,7 +58,7 @@
+ =item 1 Data syncronisity
+
+ When normal tables are updated with values that are reflected in a MV,
+-there will be a delay (usually a very noticable one) between when
++there will be a delay (usually a very noticeable one) between when
+ the normal table is updated and when the MV is updated. This tool
+ provides the means of updating the MVs; see --automatic below.
+
+--- a/load/bin/gmod_bulk_load_gff3.pl
++++ b/load/bin/gmod_bulk_load_gff3.pl
+@@ -58,7 +58,7 @@
+ to use the current directory)
+ --no_target_syn By default, the loader adds the targetId in
+ the synonyms list of the feature. This flag
+- desactivate this.
++ deactivate this.
+ --unique_target Trust the unicity of the target IDs. IDs are case
+ sensitive. By default, the uniquename of a new target
+ will be 'TargetId_PrimaryKey'. With this flag,
+@@ -224,7 +224,7 @@
+ db_name must have an entry in the db table, with a value of
+ db.name equal to 'DB:db_name'; several database names were preinstalled
+ with the database when 'make prepdb' was run. Execute 'SELECT name
+-FROM db' to find out what databases are already availble. New dbxref
++FROM db' to find out what databases are already available. New dbxref
+ entries are created in the dbxref table, and dbxrefs are linked to
+ features via the feature_dbxref table.
+
Modified: trunk/packages/gmod/chado/trunk/debian/patches/series
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/series 2011-11-09 14:04:26 UTC (rev 8493)
+++ trunk/packages/gmod/chado/trunk/debian/patches/series 2011-11-09 14:16:24 UTC (rev 8494)
@@ -1,2 +1,3 @@
fix_perl_headers
force_SIMPLE
+fix_spelling_manpage
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