[med-svn] [kineticstools] 05/05: Adapt patches and and TODO
Andreas Tille
tille at debian.org
Sat Dec 24 14:11:28 UTC 2016
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tille pushed a commit to branch master
in repository kineticstools.
commit ecf54473c81f85dc994668d74586b4cb50f96f7d
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 24 15:10:43 2016 +0100
Adapt patches and and TODO
---
debian/changelog | 3 +++
...activate-tests-requiring-unavailable-data.patch | 12 +++++-----
debian/patches/man-pages.patch | 26 +++++++++++-----------
debian/patches/verbose-testing.patch | 14 ++++++------
4 files changed, 29 insertions(+), 26 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 38186ae..07e8539 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,9 @@ kineticstools (0.6.1+dfsg-1) UNRELEASED; urgency=medium
* New upstream version
Closes: #848542
* debian/get-orig-source
+ TODO: I did not found any dependency from pybigwig but creating the documentation
+ is failing. I'm not sure whether I properly created the upstream tarball
+ and thus I'm stoping here.
-- Andreas Tille <tille at debian.org> Sat, 24 Dec 2016 08:34:57 +0100
diff --git a/debian/patches/deactivate-tests-requiring-unavailable-data.patch b/debian/patches/deactivate-tests-requiring-unavailable-data.patch
index 5c0e617..a0b5845 100644
--- a/debian/patches/deactivate-tests-requiring-unavailable-data.patch
+++ b/debian/patches/deactivate-tests-requiring-unavailable-data.patch
@@ -2,14 +2,14 @@ Description: Don't execute tests that require unavailable data files
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: not-needed
Last-Update: 2015-11-30
---- kineticstools.orig/Makefile
-+++ kineticstools/Makefile
-@@ -26,7 +26,7 @@
- tests: cram-tests unit-tests
+--- a/Makefile
++++ b/Makefile
+@@ -27,6 +27,8 @@ tests: cram-tests unit-tests extra-tests
cram-tests:
-- cram test/cram/*.t
-+ cram `ls test/cram/*.t | grep -v detection_bam`
+ cram --xunit-file=cramtests.xml test/cram/*.t
++ # this was previously in the Debian packaging
++ # cram `ls test/cram/*.t | grep -v detection_bam`
long-tests:
cram test/cram/long_running/*.t
diff --git a/debian/patches/man-pages.patch b/debian/patches/man-pages.patch
index fb0722b..85cc42b 100644
--- a/debian/patches/man-pages.patch
+++ b/debian/patches/man-pages.patch
@@ -2,8 +2,8 @@ Description: Format RST documentation into input for rst2man
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: not-needed
Last-Update: 2015-12-09
---- kineticstools.orig/doc/manual.rst
-+++ kineticstools/doc/manual.rst
+--- a/doc/manual.rst
++++ b/doc/manual.rst
@@ -1,23 +1,22 @@
+==========
+ipdSummary
@@ -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 @@
+@@ -28,8 +27,11 @@ kineticsTools also has a *Modification I
* 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
@@ -52,26 +52,26 @@ Last-Update: 2015-12-09
Algorithm
=========
-@@ -55,7 +57,6 @@
- -------------------
- 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 [...]
+@@ -69,7 +71,6 @@ With cmp.h5 input, methyl fraction calcu
+ ipdSummary aligned.cmp.h5 --reference ref.fasta --identify m6A,m4C --methylFraction --gff basemods.gff --csv kinetics.csv
+
-======
Inputs
======
-@@ -69,7 +70,6 @@
-
- The tool requires the reference sequence used to perform alignments. Currently this must be supplied via the path to a SMRTportal reference repository entry.
+@@ -85,7 +86,6 @@ Reference Sequence
+ The tool requires the reference sequence used to perform alignments. This can
+ be either a FASTA file or a ReferenceSet XML.
-=======
Outputs
=======
-@@ -178,3 +178,8 @@
- meanCoverage Mean coverage of detected instances
- objectiveScore Objective score of this motif in the motif finder algorithm
- ================== ===========
+@@ -176,3 +176,8 @@ coverage mean of case and
+ 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)
+ ================ ===========
+
+SEE ALSO
+========
diff --git a/debian/patches/verbose-testing.patch b/debian/patches/verbose-testing.patch
index 3cba59c..2a1369d 100644
--- a/debian/patches/verbose-testing.patch
+++ b/debian/patches/verbose-testing.patch
@@ -2,14 +2,14 @@ Description: Make test execution verbose
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: no
Last-Update: 2015-11-30
---- kineticstools.orig/Makefile
-+++ kineticstools/Makefile
-@@ -26,7 +26,7 @@
- tests: cram-tests unit-tests
-
+--- a/Makefile
++++ b/Makefile
+@@ -28,7 +28,7 @@ tests: cram-tests unit-tests extra-tests
cram-tests:
-- cram `ls test/cram/*.t | grep -v detection_bam`
-+ cram --verbose `ls test/cram/*.t | grep -v detection_bam`
+ cram --xunit-file=cramtests.xml test/cram/*.t
+ # this was previously in the Debian packaging
+- # cram `ls test/cram/*.t | grep -v detection_bam`
++ # cram --verbose `ls test/cram/*.t | grep -v detection_bam`
long-tests:
cram test/cram/long_running/*.t
--
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