[med-svn] [macs] 03/03: new upstream release & more spelling fixes
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 08:42:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository macs.
commit 9c99b0710de0c1bf81487156d458bed67921ca72
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon Feb 1 09:49:17 2016 -0800
new upstream release & more spelling fixes
---
debian/changelog | 7 +++++++
debian/control | 4 ++--
debian/patches/spelling | 55 +++++++++++++++++++++++++++++++++++++++++++++----
3 files changed, 60 insertions(+), 6 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 32f3859..5935113 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+macs (2.1.0.20151222-1) UNRELEASED; urgency=medium
+
+ * New upstream release
+ * A couple more spelling fixes & updated VCS URLs.
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Mon, 01 Feb 2016 09:49:01 -0800
+
macs (2.1.0.20150731-1) unstable; urgency=low
* debian/watch: now released via PyPI.
diff --git a/debian/control b/debian/control
index 8cefaff..59f4397 100644
--- a/debian/control
+++ b/debian/control
@@ -14,8 +14,8 @@ Build-Depends: debhelper (>= 9),
help2man,
cython
Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/macs.git
-Vcs-Git: git://anonscm.debian.org/debian-med/macs.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/macs.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/macs.git
Homepage: http://github.com/taoliu/MACS/
X-Python-Version: >=2.7
diff --git a/debian/patches/spelling b/debian/patches/spelling
index fa5699f..b1b67fe 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,7 +1,7 @@
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Description: Fix spelling erorr
---- macs2.orig/MACS2/PeakModel.pyx
-+++ macs2/MACS2/PeakModel.pyx
+--- macs.orig/MACS2/PeakModel.pyx
++++ macs/MACS2/PeakModel.pyx
@@ -559,7 +559,7 @@
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by introducing reflected copies of the signal
@@ -11,8 +11,26 @@ Description: Fix spelling erorr
input:
x: the input signal
---- macs2.orig/bin/macs2
-+++ macs2/bin/macs2
+--- macs.orig/bin/macs2
++++ macs/bin/macs2
+@@ -212,7 +212,7 @@
+ # group for bimodal
+ group_bimodal = argparser_callpeak.add_argument_group( "Shifting model arguments" )
+ group_bimodal.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
+- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set")
++ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set")
+ group_bimodal.add_argument( "--bw", dest = "bw", type = int, default = 300,
+ help = "Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300")
+ group_bimodal.add_argument( "-m", "--mfold", dest = "mfold", type = int, default = [5,50], nargs = 2,
+@@ -351,7 +351,7 @@
+ argparser_filterdup.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
+ help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), DEFAULT:hs" )
+ argparser_filterdup.add_argument( "-s", "--tsize", dest = "tsize", type = int,
+- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set" )
++ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set" )
+ argparser_filterdup.add_argument( "-p", "--pvalue", dest = "pvalue", type = float,
+ help = "Pvalue cutoff for binomial distribution test. DEFAULT:1e-5" )
+ argparser_filterdup.add_argument( "--keep-dup", dest = "keepduplicates", type = str, default = "auto",
@@ -370,7 +370,7 @@
"""Add function 'peak calling on bedGraph' argument parsers.
"""
@@ -58,6 +76,15 @@ Description: Fix spelling erorr
argparser_cmbreps.add_argument( "-i", dest = "ifile", type = str, required = True, nargs = "+",
help = "MACS score in bedGraph for each replicate. Require exactly two files such as '-i A B'. REQUIRED" )
# argparser_cmbreps.add_argument( "-w", dest = "weights", type = float, nargs = "*",
+@@ -492,7 +492,7 @@
+ default = None)
+ add_outdir_option( argparser_randsample )
+ argparser_randsample.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
+- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set")
++ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set")
+ argparser_randsample.add_argument( "-f", "--format", dest = "format", type = str,
+ choices=("AUTO","BAM","SAM","BED","ELAND","ELANDMULTI","ELANDEXPORT","BOWTIE"),
+ help = "Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or \"BOWTIE\". The default AUTO option will %(prog)s decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: \"AUTO\"",
@@ -503,7 +503,7 @@
def add_bdgdiff_parser( subparsers ):
@@ -67,3 +94,23 @@ Description: Fix spelling erorr
argparser_bdgdiff.add_argument( "--t1", dest = "t1bdg", type = str, required = True,
help = "MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED" )
argparser_bdgdiff.add_argument( "--t2", dest="t2bdg", type = str, required = True,
+@@ -572,7 +572,7 @@
+ argparser_predictd.add_argument( "-g", "--gsize", dest = "gsize", type = str, default = "hs",
+ help = "Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs" )
+ argparser_predictd.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
+- help = "Tag size. This will overide the auto detected tag size. DEFAULT: Not set")
++ help = "Tag size. This will override the auto detected tag size. DEFAULT: Not set")
+ argparser_predictd.add_argument( "--bw", dest = "bw", type = int, default = 300,
+ help = "Band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300")
+ argparser_predictd.add_argument( "-m", "--mfold", dest = "mfold", type = int, default = [5,50], nargs = 2,
+--- macs.orig/MACS2/IO/FixWidthTrack.pyx
++++ macs/MACS2/IO/FixWidthTrack.pyx
+@@ -954,7 +954,7 @@
+ values. Final pileup will the maximum.
+ scale_factor_s : linearly scale the pileup value applied to each d in ds. The list should have the same length as ds.
+ baseline_value : a value to be filled for missing values, and will be the minimum pileup.
+- directional : if False, the strand or direction of tag will be ignored, so that extenstion will be both sides with d/2.
++ directional : if False, the strand or direction of tag will be ignored, so that extension will be both sides with d/2.
+ end_shift : move cutting ends towards 5->3 direction if value is positive, or towards 3->5 direction if negative. Default is 0 -- no shift at all.
+
+
--
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