[med-svn] [kineticstools] 04/04: fix man page building

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository kineticstools.

commit 56460c100326f14358fd0a21d2f4226b4ad22bc1
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sat Jan 14 13:22:11 2017 +0000

    fix man page building
---
 debian/patches/man-pages.patch | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/debian/patches/man-pages.patch b/debian/patches/man-pages.patch
index 85cc42b..baed4a4 100644
--- a/debian/patches/man-pages.patch
+++ b/debian/patches/man-pages.patch
@@ -39,7 +39,7 @@ Last-Update: 2015-12-09
  Modification Detection
  ----------------------
  The basic mode of kineticsTools does an independent comparison of IPDs at each position on the genome, for each strand, and emits various statistics to CSV and GFF (after applying a significance filter).
-@@ -28,8 +27,11 @@ kineticsTools also has a *Modification I
+@@ -28,8 +27,11 @@
   * Different modifications occuring on the same base can be distinguished (for example m5C and m4C)
   * The signal from one modification is combined into one statistic, improving sensitivity, removing extra peaks, and correctly centering the call
  
@@ -52,7 +52,15 @@ Last-Update: 2015-12-09
  Algorithm
  =========
  
-@@ -69,7 +71,6 @@ With cmp.h5 input, methyl fraction calcu
+@@ -56,7 +58,6 @@
+ We test the hypothesis that IPDs observed at a particular locus in the sample have a longer means than IPDs observed at the same locus in unmodified DNA.  If we have generated a Whole Genome Amplified dataset, which removes DNA modifications, we use a case-control, two-sample t-test.  This tool also provides a pre-calibrated 'synthetic control' model which predicts the unmodified IPD, given a 12 base sequence context. In the synthetic control case we use a one-sample t-test, with an adj [...]
+ 
+ 
+-=============
+ Example Usage
+ =============
+ 
+@@ -69,7 +70,6 @@
    ipdSummary aligned.cmp.h5 --reference ref.fasta --identify m6A,m4C --methylFraction --gff basemods.gff --csv kinetics.csv
  
  
@@ -60,7 +68,7 @@ Last-Update: 2015-12-09
  Inputs
  ======
  
-@@ -85,7 +86,6 @@ Reference Sequence
+@@ -85,7 +85,6 @@
  The tool requires the reference sequence used to perform alignments.  This can
  be either a FASTA file or a ReferenceSet XML.
  
@@ -68,7 +76,7 @@ Last-Update: 2015-12-09
  Outputs
  =======
  
-@@ -176,3 +176,8 @@ coverage                mean of case and
+@@ -176,3 +175,8 @@
  controlCoverage         count of valid control IPDs at this position (see Filtering section for details)
  caseCoverage            count of valid case IPDs at this position (see Filtering section for details)
  ================	===========

-- 
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