[med-svn] [macs] 03/03: new upstream version
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue May 24 11:02:39 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 adcd9966bb4e77552b6900d9d0a8dfec1d1a273b
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Fri May 13 09:50:00 2016 -0700
new upstream version
---
debian/changelog | 9 +++
debian/control | 4 +-
debian/patches/spelling | 143 ++++++++++--------------------------------------
debian/rules | 1 +
4 files changed, 42 insertions(+), 115 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index ff2402f..4311a55 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+macs (2.1.1.20160309-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Bump Standards-Version to 3.9.8
+ * Refresh & re-submit spelling patch
+ * enable "bindnow" linker flag hardening
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 13 May 2016 10:49:54 -0700
+
macs (2.1.1.20160226-1) unstable; urgency=medium
* New upstream release
diff --git a/debian/control b/debian/control
index e1c1710..2417808 100644
--- a/debian/control
+++ b/debian/control
@@ -1,6 +1,6 @@
Source: macs
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>,
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Tim Booth <tbooth at ceh.ac.uk>,
H. Soon Gweon <hyugwe at ceh.ac.uk>,
Andreas Tille <tille at debian.org>
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 9),
python-setuptools,
help2man,
cython
-Standards-Version: 3.9.7
+Standards-Version: 3.9.8
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 fe51f19..f8a4aa4 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,118 +1,35 @@
From: Michael R. Crusoe <crusoe at ucdavis.edu>
Subject: Fix spelling erorr
-Forwarded: https://github.com/taoliu/MACS/pull/120
+Forwarded: https://github.com/taoliu/MACS/pull/129
---- 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
- (with the window size) in both ends so that transient parts are minimized
-- in the begining and end part of the output signal.
-+ in the beginning and end part of the output signal.
-
- input:
- x: the input signal
---- macs.orig/bin/macs2
-+++ macs/bin/macs2
-@@ -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,
-- 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,
-@@ -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,
-- 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",
-@@ -373,7 +373,7 @@
- """Add function 'peak calling on bedGraph' argument parsers.
- """
- argparser_bdgpeakcall = subparsers.add_parser( "bdgpeakcall",
-- help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
-+ help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
- 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,
-@@ -398,7 +398,7 @@
- """Add function 'broad peak calling on bedGraph' argument parsers.
- """
- argparser_bdgbroadcall = subparsers.add_parser( "bdgbroadcall",
-- help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
-+ help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
- 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,
-@@ -421,7 +421,7 @@
- """Add function 'peak calling on bedGraph' argument parsers.
- """
- argparser_bdgcmp = subparsers.add_parser( "bdgcmp",
-- help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
-+ help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
- 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,
-@@ -447,7 +447,7 @@
- """Add function 'operations on score column of bedGraph' argument parsers.
- """
- argparser_bdgopt = subparsers.add_parser( "bdgopt",
-- help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
-+ help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
- 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,
-@@ -464,7 +464,7 @@
- """Add function 'combine replicates' argument parsers.
- """
- argparser_cmbreps = subparsers.add_parser( "cmbreps",
-- help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
-+ help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
- 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 = "*",
-@@ -495,7 +495,7 @@
- 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\"",
-@@ -506,7 +506,7 @@
-
- def add_bdgdiff_parser( subparsers ):
- argparser_bdgdiff = subparsers.add_parser( "bdgdiff",
-- help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
-+ help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
- 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,
-@@ -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,
-- 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.
+--- macs.orig/MACS2/Pileup.pyx
++++ macs/MACS2/Pileup.pyx
+@@ -175,7 +175,7 @@
+ trackI : A FWTrack object with raw plus and minus 5' end positions
+ d : tag will be extended to this value to 3' direction, unless directional is False.
+ baseline_value : a value to be filled for missing values.
+- 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.
+ halfextension: only make a fragment of d/2 size centered at fragment center
+ Return a bedGraphTrackI object.
+@@ -237,7 +237,7 @@
+ trackI : A FWTrack object with raw plus and minus 5' end positions
+ d : tag will be extended to this value to 3' direction, unless directional is False.
+ baseline_value : a value to be filled for missing values.
+- 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.
+ halfextension: only make a fragment of d/2 size centered at fragment center
+ Return a bedGraphTrackI object.
+--- macs.orig/MACS2/IO/PeakIO.pyx
++++ macs/MACS2/IO/PeakIO.pyx
+@@ -548,7 +548,7 @@
+
+ def overlap_with_other_peaks (self, peaks2, double cover=0):
+ """Peaks2 is a PeakIO object or dictionary with can be
+- initialzed as a PeakIO. check __init__ for PeakIO for detail.
++ initialized as a PeakIO. check __init__ for PeakIO for detail.
+
+ return how many peaks are intersected by peaks2 by percentage
+ coverage on peaks2(if 50%, cover = 0.5).
diff --git a/debian/rules b/debian/rules
index 9076306..3569773 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,7 @@
#!/usr/bin/make -f
export PYBUILD_NAME=MACS2
+export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
subcommands=callpeak bdgpeakcall bdgbroadcall bdgcmp bdgopt cmbreps bdgdiff \
--
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