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commit adcd9966bb4e77552b6900d9d0a8dfec1d1a273b Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> 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 <[email protected]> -Uploaders: Michael R. Crusoe <[email protected]>, +Uploaders: Michael R. Crusoe <[email protected]>, Tim Booth <[email protected]>, H. Soon Gweon <[email protected]>, Andreas Tille <[email protected]> @@ -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 <[email protected]> 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 \ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/macs.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
