[med-svn] [macs] 03/03: bump version & refresh spelling patch
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Mar 5 17:54:16 UTC 2016
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misterc-guest pushed a commit to branch master
in repository macs.
commit 20503bfaa51d1b1795a0fe9ff931a16435428837
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Mar 5 09:25:31 2016 -0800
bump version & refresh spelling patch
---
debian/changelog | 6 ++++++
debian/control | 2 +-
debian/patches/spelling | 26 ++++++++++++++------------
3 files changed, 21 insertions(+), 13 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 5aae862..ff2402f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+macs (2.1.1.20160226-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Sat, 05 Mar 2016 09:53:12 -0800
+
macs (2.1.0.20151222-1) unstable; urgency=medium
* New upstream release
diff --git a/debian/control b/debian/control
index 59f4397..e1c1710 100644
--- a/debian/control
+++ b/debian/control
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 9),
python-setuptools,
help2man,
cython
-Standards-Version: 3.9.6
+Standards-Version: 3.9.7
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/
diff --git a/debian/patches/spelling b/debian/patches/spelling
index b1b67fe..fe51f19 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,5 +1,7 @@
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
-Description: Fix spelling erorr
+From: Michael R. Crusoe <crusoe at ucdavis.edu>
+Subject: Fix spelling erorr
+Forwarded: https://github.com/taoliu/MACS/pull/120
+
--- macs.orig/MACS2/PeakModel.pyx
+++ macs/MACS2/PeakModel.pyx
@@ -559,7 +559,7 @@
@@ -13,7 +15,7 @@ Description: Fix spelling erorr
x: the input signal
--- macs.orig/bin/macs2
+++ macs/bin/macs2
-@@ -212,7 +212,7 @@
+@@ -213,7 +213,7 @@
# 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,
@@ -22,7 +24,7 @@ Description: Fix spelling erorr
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 @@
+@@ -354,7 +354,7 @@
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,
@@ -31,7 +33,7 @@ Description: Fix spelling erorr
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 @@
+@@ -373,7 +373,7 @@
"""Add function 'peak calling on bedGraph' argument parsers.
"""
argparser_bdgpeakcall = subparsers.add_parser( "bdgpeakcall",
@@ -40,7 +42,7 @@ Description: Fix spelling erorr
argparser_bdgpeakcall.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
help = "MACS score in bedGraph. REQUIRED" )
argparser_bdgpeakcall.add_argument( "-c", "--cutoff" , dest = "cutoff", type = float,
-@@ -395,7 +395,7 @@
+@@ -398,7 +398,7 @@
"""Add function 'broad peak calling on bedGraph' argument parsers.
"""
argparser_bdgbroadcall = subparsers.add_parser( "bdgbroadcall",
@@ -49,7 +51,7 @@ Description: Fix spelling erorr
argparser_bdgbroadcall.add_argument( "-i", "--ifile", dest = "ifile" , type = str, required = True,
help = "MACS score in bedGraph. REQUIRED" )
argparser_bdgbroadcall.add_argument( "-c", "--cutoff-peak", dest = "cutoffpeak", type = float,
-@@ -418,7 +418,7 @@
+@@ -421,7 +421,7 @@
"""Add function 'peak calling on bedGraph' argument parsers.
"""
argparser_bdgcmp = subparsers.add_parser( "bdgcmp",
@@ -58,7 +60,7 @@ Description: Fix spelling erorr
argparser_bdgcmp.add_argument( "-t", "--tfile", dest = "tfile", type = str, required = True,
help = "Treatment bedGraph file, e.g. *_treat_pileup.bdg from MACSv2. REQUIRED")
argparser_bdgcmp.add_argument( "-c", "--cfile", dest = "cfile", type = str, required = True,
-@@ -444,7 +444,7 @@
+@@ -447,7 +447,7 @@
"""Add function 'operations on score column of bedGraph' argument parsers.
"""
argparser_bdgopt = subparsers.add_parser( "bdgopt",
@@ -67,7 +69,7 @@ Description: Fix spelling erorr
argparser_bdgopt.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
help = "MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED" )
argparser_bdgopt.add_argument( "-m", "--method", dest = "method", type = str,
-@@ -461,7 +461,7 @@
+@@ -464,7 +464,7 @@
"""Add function 'combine replicates' argument parsers.
"""
argparser_cmbreps = subparsers.add_parser( "cmbreps",
@@ -76,7 +78,7 @@ 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 @@
+@@ -495,7 +495,7 @@
default = None)
add_outdir_option( argparser_randsample )
argparser_randsample.add_argument( "-s", "--tsize", dest = "tsize", type = int, default = None,
@@ -85,7 +87,7 @@ Description: Fix spelling erorr
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 @@
+@@ -506,7 +506,7 @@
def add_bdgdiff_parser( subparsers ):
argparser_bdgdiff = subparsers.add_parser( "bdgdiff",
@@ -94,7 +96,7 @@ 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 @@
+@@ -575,7 +575,7 @@
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,
--
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