[Debian-med-packaging] [SCM] gmap branch, master, updated. upstream/2010-07-21-12-g11dc610

[Shaun Jackman]

The following commit has been merged in the master branch:
commit 11dc6102443b13a5b00b2d4a1d758a16f73093fd
Author: Shaun Jackman <sjackman at debian.org>
Date:   Thu Jul 22 11:58:16 2010 -0700

    * debian/gmap.1: Remove double spaces.
    * debian/gmap_setup.1: Ditto.
    * debian/gsnap.1: Ditto.

diff --git a/debian/gmap.1 b/debian/gmap.1
index 0da5261..7ac4568 100644
--- a/debian/gmap.1
+++ b/debian/gmap.1
@@ -15,7 +15,7 @@ With no QUERY, read standard input.
 Genome directory
 .TP
 \fB\-d\fR, \fB\-\-db\fR=\fISTRING\fR
-Genome database.  If argument is '?' (with
+Genome database. If argument is '?' (with
 the quotes), this command lists available databases.
 .TP
 \fB\-G\fR, \fB\-\-genomefull\fR
@@ -117,7 +117,7 @@ Format for output
 Output options
 .TP
 \fB\-n\fR, \fB\-\-npaths\fR=\fIINT\fR
-Maximum number of paths to show.  If set to 0,
+Maximum number of paths to show. If set to 0,
 prints two paths if chimera detected, else one.
 .TP
 \fB\-O\fR, \fB\-\-ordered\fR
@@ -150,7 +150,7 @@ External map file options
 Map directory
 .TP
 \fB\-m\fR, \fB\-\-map\fR=\fIiitfile\fR
-Map file.  If argument is '?' (with the quotes),
+Map file. If argument is '?' (with the quotes),
 this lists available map files.
 .TP
 \fB\-e\fR, \fB\-\-mapexons\fR
diff --git a/debian/gmap_setup.1 b/debian/gmap_setup.1
index e73bf68..83e73e4 100644
--- a/debian/gmap_setup.1
+++ b/debian/gmap_setup.1
@@ -47,8 +47,8 @@ like this:
 gmap_setup \fB\-d\fR <genome> <fasta_file>...
 .PP
 The accession of each FASTA header (the word following each ">") will
-be the name of each chromosome.  GMAP can handle an unlimited number
-of "chromosomes", with arbitrarily long names.  In this way, GMAP
+be the name of each chromosome. GMAP can handle an unlimited number
+of "chromosomes", with arbitrarily long names. In this way, GMAP
 could be used as a general search program for near\-identity matches
 against a FASTA file.
 .TP
@@ -57,7 +57,7 @@ If your sequences represent contigs that have
 mapping information to specific chromosomal regions, then you can
 have gmap_setup try to read each header to determine its chromosomal
 region (the \fB\-C\fR flag) or read an .md file that contains information
-about chromosomal regions (the \fB\-M\fR flag).  The .md files are often
+about chromosomal regions (the \fB\-M\fR flag). The .md files are often
 provided in NCBI releases, but since the formats change often,
 gmap_setup will prompt you to make sure it parses it correctly.
 .TP
@@ -74,11 +74,11 @@ examples:
 \fB\-W\fR
 The gmap_setup process works best if you have a
 computer with enough RAM to hold the entire genome (e.g., 3
-gigabytes for a human\- or mouse\-sized genome).  Since the resulting
+gigabytes for a human\- or mouse\-sized genome). Since the resulting
 genome files work across all machine architectures, you can find any
 machine with sufficient RAM to build the genome files and then
-transfer the files to another machine.  (GMAP itself runs fine on
-machines with limited RAM.)  If you cannot find any machine with
+transfer the files to another machine. (GMAP itself runs fine on
+machines with limited RAM.) If you cannot find any machine with
 sufficient RAM for gmap_setup, you can run the program with the \fB\-W\fR
 flag to write the files directly, but this can be very slow.
 .TP
@@ -86,8 +86,8 @@ flag to write the files directly, but this can be very slow.
 If you specify a smaller interval (for example,
 3 for the GMAP interval), you can create a higher\-resolution
 database, which can be useful for mapping small oligomers (smaller
-than 18 nt).  However, the corresponding genome index files will be
-larger (twice as big if you specify \fB\-q\fR 3).  These index files may
+than 18 nt). However, the corresponding genome index files will be
+larger (twice as big if you specify \fB\-q\fR 3). These index files may
 exceed the 2 gigabyte file offset limit on some computers, and will
 therefore fail to work on those computers.
 .SH AUTHOR
diff --git a/debian/gsnap.1 b/debian/gsnap.1
index 7ab6da9..9dc5fda 100644
--- a/debian/gsnap.1
+++ b/debian/gsnap.1
@@ -27,7 +27,7 @@ Circular\-end data (paired reads are on same strand)
 Computation options
 .PP
 Note: GSNAP has an ultrafast algorithm for calculating mismatches up to and including
-((readlength+2)/12 \- 2) ("ultrafast mismatches").  The program will run fastest if
+((readlength+2)/12 \- 2) ("ultrafast mismatches"). The program will run fastest if
 max\-mismatches (plus suboptimal\-levels) is within that value.
 Also, indels, especially end indels, take longer to compute, although the algorithm
 is still designed to be fast.
@@ -40,14 +40,14 @@ Batch mode (0 = no pre\-loading, 1 = pre\-load only indices;
 Maximum number of mismatches allowed (if not specified, then
 defaults to the ultrafast level of ((readlength+2)/12 \- 2))
 If specified between 0.0 and 1.0, then treated as a fraction
-of each read length.  Otherwise, treated as an integral number
+of each read length. Otherwise, treated as an integral number
 of mismatches (including indel and splicing penalties)
 For RNA-Seq, you may need to increase this value to 10 or so,
 to align reads extending past the ends of an exon.
 .TP
 \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR
 Penalty for an indel (default 1000, essentially turning it off).
-Counts against mismatches allowed.  To find indels, make
+Counts against mismatches allowed. To find indels, make
 indel\-penalty less than or equal to max\-mismatches
 For 2\-base reads, need to set indel\-penalty somewhat high
 .TP
@@ -100,7 +100,7 @@ previously using snpindex) for tolerance to SNPs
 .TP
 \fB\-g\fR, \fB\-\-geneprob\fR=\fISTRING\fR
 Use IIT file containing geneprob (in <STRING>.iit, of cumulative
-format  >(count) (genomicpos)  to resolve ties
+format >(count) (genomicpos) to resolve ties
 .TP
 \fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR
 Number of worker threads
@@ -139,7 +139,7 @@ Options for paired\-end reads
 .TP
 \fB\-P\fR, \fB\-\-pairmax\fR=\fIINT\fR
 Max total genomic length for paired reads
-(default 1000).  Should increase for RNA\-Seq reads.
+(default 1000). Should increase for RNA\-Seq reads.
 .TP
 \fB\-p\fR, \fB\-\-pairlength\fR=\fIINT\fR
 Expected paired\-end length (default 200)

-- 
Align mRNA and EST sequences to a genome