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haplohseq: Identify regions of allelic imbalance
Module Name: pkgsrc-wip
Committed By: Jason W Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Sat Jan 23 13:24:12 2021 -0600
Changeset: 12bbf93b90442ccf109df0d5430d5f8a244ace6d
Modified Files:
Makefile
Added Files:
haplohseq/DESCR
haplohseq/Makefile
haplohseq/PLIST
haplohseq/distinfo
haplohseq/files/haplohseq-example.in
haplohseq/files/run-tests
haplohseq/patches/patch-makefile
haplohseq/patches/patch-scripts_ldmap.py
haplohseq/patches/patch-scripts_simple__phaser.py
haplohseq/patches/patch-src_FreqPhase.cpp
haplohseq/patches/patch-src_HaplohSeq.cpp
haplohseq/patches/patch-src_test_InputProcessorTest.cpp
Log Message:
haplohseq: Identify regions of allelic imbalance
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=12bbf93b90442ccf109df0d5430d5f8a244ace6d
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
haplohseq/DESCR | 4 +
haplohseq/Makefile | 55 +++++++++++
haplohseq/PLIST | 9 ++
haplohseq/distinfo | 12 +++
haplohseq/files/haplohseq-example.in | 37 +++++++
haplohseq/files/run-tests | 10 ++
haplohseq/patches/patch-makefile | 109 +++++++++++++++++++++
haplohseq/patches/patch-scripts_ldmap.py | 46 +++++++++
haplohseq/patches/patch-scripts_simple__phaser.py | 35 +++++++
haplohseq/patches/patch-src_FreqPhase.cpp | 33 +++++++
haplohseq/patches/patch-src_HaplohSeq.cpp | 24 +++++
.../patches/patch-src_test_InputProcessorTest.cpp | 15 +++
13 files changed, 390 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 0441a1bcf7..fccad3553a 100644
--- a/Makefile
+++ b/Makefile
@@ -1426,6 +1426,7 @@ SUBDIR+= hal
SUBDIR+= halfempty
SUBDIR+= hammer
SUBDIR+= hanazono-ttf
+SUBDIR+= haplohseq
SUBDIR+= harmony
SUBDIR+= hasciicam
SUBDIR+= haserl
diff --git a/haplohseq/DESCR b/haplohseq/DESCR
new file mode 100644
index 0000000000..57173a7ea3
--- /dev/null
+++ b/haplohseq/DESCR
@@ -0,0 +1,4 @@
+Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
+obtained from impure samples where AI events exist in a potentially low
+proportion of cells in the sample. Input to the software includes a VCF file
+of genotypes and estimated phased genotypes.
diff --git a/haplohseq/Makefile b/haplohseq/Makefile
new file mode 100644
index 0000000000..3aa3685fc2
--- /dev/null
+++ b/haplohseq/Makefile
@@ -0,0 +1,55 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Sat Jan 23 09:24:36 CST 2021 #
+###########################################################
+
+# Unknown tool: USE_TOOLS= compiler:c++11-lang
+# Unknown tool: USE_TOOLS= localbase:ldflags
+
+DISTNAME= haplohseq-0.1.2
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_PROJECT= haplohseq
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://sites.google.com/site/integrativecancergenomics/software/haplohseq
+COMMENT= Identify regions of allelic imbalance
+LICENSE= mit
+
+# math/R is blocked by glib2 build error on CentOS
+# DEPENDS= R-cran-optparse>0:../../wip/R-optparse
+
+REPLACE_SH= example/example_run.sh
+
+SUBST_CLASSES+= test
+SUBST_STAGE.test= pre-configure
+SUBST_SED.test= -e 's|\.\./haplohseq|haplohseq|'
+SUBST_SED.test+= -e 's|python|mkdir example_output; ${PYTHONBIN}|'
+SUBST_FILES.test= example/example_run.sh
+
+USE_LANGUAGES= c c++
+USE_TOOLS+= gmake pax
+MAKE_FILE= makefile
+# Check this
+# MAKE_ENV+= STRIP=${STRIP}
+
+EXAMPLESDIR= ${PREFIX}/share/examples/haplohseq
+
+INSTALLATION_DIRS= share/examples/haplohseq
+
+post-patch:
+ ${SED} -e "s|%%EXAMPLESDIR%%|${EXAMPLESDIR}|" \
+ ${FILESDIR}/haplohseq-example.in > ${WRKDIR}/haplohseq-example
+
+post-install:
+ ${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${DESTDIR}${PREFIX}/bin
+ (cd ${WRKSRC} && ${RM} scripts/*.orig && pax -rw example ldmap scripts ${DESTDIR}${EXAMPLESDIR})
+
+do-test:
+ (cd ${WRKSRC}/build/test && ${SH} ${FILESDIR}/run-tests)
+
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/haplohseq/PLIST b/haplohseq/PLIST
new file mode 100644
index 0000000000..fca48e502f
--- /dev/null
+++ b/haplohseq/PLIST
@@ -0,0 +1,9 @@
+@comment $NetBSD$
+bin/haplohseq
+bin/haplohseq-example
+share/examples/haplohseq/example/example_input/tumor_exome.vcf
+share/examples/haplohseq/example/example_run.sh
+share/examples/haplohseq/ldmap/hg19.exome.ldmap
+share/examples/haplohseq/scripts/haplohseq_plot.R
+share/examples/haplohseq/scripts/ldmap.py
+share/examples/haplohseq/scripts/simple_phaser.py
diff --git a/haplohseq/distinfo b/haplohseq/distinfo
new file mode 100644
index 0000000000..2ba38bf958
--- /dev/null
+++ b/haplohseq/distinfo
@@ -0,0 +1,12 @@
+$NetBSD$
+
+SHA1 (haplohseq-0.1.2.tar.gz) = 58ef6a985c48c66bb3e824cfa903d7f63da128c2
+RMD160 (haplohseq-0.1.2.tar.gz) = 8287c3323d2bb6bee2146ce56d20ab5fb31cca80
+SHA512 (haplohseq-0.1.2.tar.gz) = 922f04203b148e52daf672b2f9d780a68a1709c9d907e76bd37841d22cbe4b4175cce7004fb38547dbc4724061db2a11755e292f0dec0b67a71f748fdb009eba
+Size (haplohseq-0.1.2.tar.gz) = 12084603 bytes
+SHA1 (patch-makefile) = 3fbba14e82d35488b7f5c1838a9b6891b6f1e2f5
+SHA1 (patch-scripts_ldmap.py) = bc66e0b1b5e40c59068ffd3b33267a97d7b3a50c
+SHA1 (patch-scripts_simple__phaser.py) = 33f2c6a6b70d236404725179629129f81607cbd7
+SHA1 (patch-src_FreqPhase.cpp) = 5b906e53f2e6968525bd4b1c420d518260388381
+SHA1 (patch-src_HaplohSeq.cpp) = cac07999985c5d45e9afc37b9afcddb217e0d701
+SHA1 (patch-src_test_InputProcessorTest.cpp) = 1a1086b082b542266a1e3509f0e833dcdb1038cb
diff --git a/haplohseq/files/haplohseq-example.in b/haplohseq/files/haplohseq-example.in
new file mode 100644
index 0000000000..0cb2a5bee1
--- /dev/null
+++ b/haplohseq/files/haplohseq-example.in
@@ -0,0 +1,37 @@
+#!/bin/sh -e
+
+##########################################################################
+# Script description:
+# Run haplohseq example
+#
+# https://sites.google.com/site/integrativecancergenomics/software/haplohseq
+#
+# History:
+# Date Name Modification
+# 2019-11-13 Jason Bacon Begin
+##########################################################################
+
+usage()
+{
+ printf "Usage: $0 directory\n"
+ exit 1
+}
+
+
+##########################################################################
+# Main
+##########################################################################
+
+if [ $# != 1 ]; then
+ usage
+fi
+
+dir="$1"
+
+if [ -e "$dir" ]; then
+ printf "'$dir' already exists. Please remove it or specify another.\n"
+ exit 1
+fi
+cp -R %%EXAMPLESDIR%% "$dir"
+cd "$dir/example"
+sh ./example_run.sh
diff --git a/haplohseq/files/run-tests b/haplohseq/files/run-tests
new file mode 100644
index 0000000000..1ecc6ebc5e
--- /dev/null
+++ b/haplohseq/files/run-tests
@@ -0,0 +1,10 @@
+#!/bin/sh -e
+
+printf "\n=== FreqPhaseTest ===\n\n"
+./FreqPhaseTest
+printf "\n=== InputProcessorTest ===\n\n"
+./InputProcessorTest
+printf "\n=== HmmTest ===\n\n"
+./HmmTest
+printf "\n=== HaplohSeqTest ===\n\n"
+./HaplohSeqTest
diff --git a/haplohseq/patches/patch-makefile b/haplohseq/patches/patch-makefile
new file mode 100644
index 0000000000..d7d1bdfc19
--- /dev/null
+++ b/haplohseq/patches/patch-makefile
@@ -0,0 +1,109 @@
+$NetBSD$
+
+# Respect env, add destdir support
+
+--- makefile.orig 2019-08-29 18:03:23 UTC
++++ makefile
+@@ -7,23 +7,32 @@
+ #
+
+ # Constants
+-CXX=g++
++# Default to g++ if not set by make args or environment
++CXX?=g++
+ #-O0 -g will turn on debugging
+ #The rule of thumb:
+ #When you need to debug, use -O0 (and -g to generate debugging symbols.)
+ #When you are preparing to ship it, use -O2.
+ #When you use gentoo, use -O3...!
+ #When you need to put it on an embedded system, use -Os (optimize for size, not for efficiency.)
+-CXX_FLAGS=-Wall -g -stdlib=libstdc++
++# Use canonincal compiler variables, which may be provided by build env
++CXXFLAGS?=-Wall -g -stdlib=libstdc++
+ SRC=src
+ CONF=conf
+ HMM_SRC=$(SRC)/hmm
+ UTIL_SRC=$(SRC)/util
+-BOOST=/usr/local/boost_1_52_0
++BOOST?=/usr/local/boost_1_52_0
+ INCLUDES=-I./$(SRC) -I./$(HMM_SRC) -I./$(UTIL_SRC) -isystem$(BOOST)
+-LIBRARY_PATHS=-Llib/macosx
++LIBRARY_PATHS?=-Llib/macosx
+ LIBRARIES=-lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread
+
++# Installation target with destdir support
++DESTDIR?=.
++PREFIX?=/usr/local
++MKDIR?=mkdir
++INSTALL?=install
++STRIP?= # empty, set to -s to install stripped binary
++
+ # Generated directories which are generated in this script and cleaned up with 'make clean'
+ BUILD=build
+ OBJ=$(BUILD)/obj
+@@ -35,18 +44,21 @@ directories:
+
+ # Create object files into the OBJ directory from cpp files in the SRC directory.
+ $(OBJ)/%.o: $(SRC)/%.cpp directories
+- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
++ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
+ $(OBJ)/%.o: $(HMM_SRC)/%.cpp directories
+- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
++ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
+ $(OBJ)/%.o: $(UTIL_SRC)/%.cpp directories
+- $(CXX) $(CXX_FLAGS) $(INCLUDES) -c -o $@ $<
++ $(CXX) $(CXXFLAGS) $(INCLUDES) -c -o $@ $<
+
+-all: clean haplohseq
++all: haplohseq test
+
+ haplohseq: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o
+- $(CXX) -o $(BIN)/$@ $(CXX_FLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES)
+- cp -r $(CONF) $(BIN)/.
+-
++ $(CXX) -o $(BIN)/$@ $(CXXFLAGS) $(INCLUDES) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/Reporter.o $(OBJ)/FreqPhase.o $(OBJ)/VcfUtil.o $(OBJ)/HaplohSeq.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
++
++install:
++ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++ $(INSTALL) -c $(STRIP) $(BIN)/* $(DESTDIR)$(PREFIX)/bin
++
+ clean:
+ rm -rf $(BUILD)
+
+@@ -74,28 +86,28 @@ test: FreqPhaseTest HaplohSeqTest HmmTest InputProcess
+
+ # Create test object files into the OBJ directory from cpp files in the SRC directory.
+ $(TEST_BIN)/%.o: $(TEST_SRC)/%.cpp directories test_directory
+- $(CXX) $(CXX_FLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $<
++ $(CXX) $(CXXFLAGS) $(INCLUDES) $(TEST_INCLUDES) -c -o $@ $<
+
+ HaplohSeqTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/HaplohSeqTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+ FreqPhaseTest: $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(OBJ)/FreqPhase.o $(TEST_BIN)/FreqPhaseTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+ HmmTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/HmmTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+ InputProcessorTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/InputProcessor.o $(TEST_BIN)/InputProcessorTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+ MathUtilTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/MathUtilTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+ ReporterTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(TEST_BIN)/ReporterTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+
+ ThreadPoolTest: $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o
+- $(CXX) -o $(TEST_BIN)/$@ $(CXX_FLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES)
++ $(CXX) -o $(TEST_BIN)/$@ $(CXXFLAGS) $(OBJ)/Hmm.o $(OBJ)/DataStructures.o $(OBJ)/MathUtil.o $(OBJ)/StringUtil.o $(OBJ)/ThreadPool.o $(TEST_BIN)/ThreadPoolTest.o $(LIBRARY_PATHS) $(LIBRARIES) $(LDFLAGS)
+ ############################## END TEST LOGIC ##############################
+
+
diff --git a/haplohseq/patches/patch-scripts_ldmap.py b/haplohseq/patches/patch-scripts_ldmap.py
new file mode 100644
index 0000000000..e868ab6704
--- /dev/null
+++ b/haplohseq/patches/patch-scripts_ldmap.py
@@ -0,0 +1,46 @@
+$NetBSD$
+
+# Python 3
+
+--- scripts/ldmap.py.orig 2021-01-23 17:32:15 UTC
++++ scripts/ldmap.py
+@@ -29,10 +29,10 @@ class MapMaker:
+ coordinates of the haplotype marker genomic positions.
+ '''
+ def __init__(self, markerFilename, haplotypesFilename):
+- print "reading haplotype base coordinates ...."
++ print("reading haplotype base coordinates ....")
+ self.coords, self.coordIndexes, self.refs, self.alts = self.readMarkers(markerFilename)
+ # self.haplotypes = self.readHaplotypes(haplotypesFilename)
+- print "reading haplotype panel ...."
++ print("reading haplotype panel ....")
+ self.markerCalls = self.readHaplotypes(haplotypesFilename, transpose = True)
+
+ # reads from a vcf file of defined positions representing the haplotype data
+@@ -118,7 +118,7 @@ class MapMaker:
+ # 1) COLLECT MARGINALS AND IDENTIFY SITES THAT ARE POLYMORPHIC
+ # If a site has only one allele in the haplotype panel it is not informative, so it won't be used
+ # in LD calculations. We may want to consider setting some minimum threshold for a minor allele frequency.
+- print "collecting marginal allele counts and identifying polymorphic sites from haplotype panel ...."
++ print("collecting marginal allele counts and identifying polymorphic sites from haplotype panel ....")
+ for index in range(0,len(self.markerCalls)):
+ ref = self.refs[index]
+ alt = self.alts[index]
+@@ -152,7 +152,7 @@ class MapMaker:
+ log.write("Num non-polymorphic sites: " + str(numNonpolymorphicSites) + "\n")
+
+ # 2) CALCULATE D FOR POLYMORPHIC SITES COMPARED WITH N SITES TO THE RIGHT THAT ARE POLYMORPHIC
+- print "calculating D between polymorphic sites and their neighbors ...."
++ print("calculating D between polymorphic sites and their neighbors ....")
+ dVals = []
+ for i in range(0, len(polymorphicIndexes)): # the last coordinate won't have any partners
+ index_i = polymorphicIndexes[i]
+@@ -244,7 +244,7 @@ class LDMap:
+ return ldMap
+
+ def save(self, filename):
+- print "saving ldmap to " + filename
++ print("saving ldmap to " + filename)
+ ldMapFile = open(filename, 'w')
+ ldMapFile.write("\t".join(["COORD","REF","ALT","PAIRED_ALLELES"]) + "\n")
+ for i in range(0,len(self.coords)):
diff --git a/haplohseq/patches/patch-scripts_simple__phaser.py b/haplohseq/patches/patch-scripts_simple__phaser.py
new file mode 100644
index 0000000000..1aa33ee892
--- /dev/null
+++ b/haplohseq/patches/patch-scripts_simple__phaser.py
@@ -0,0 +1,35 @@
+$NetBSD$
+
+# Python 3
+
+--- scripts/simple_phaser.py.orig 2021-01-23 17:25:56 UTC
++++ scripts/simple_phaser.py
+@@ -108,7 +108,7 @@ class SimplePhaser:
+ return informativeHets, informativeCoords, informativeIndexes
+
+ def getRefPairedAllele(self, anchorIndex, pairedIndex):
+-# print "\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts
++# print("\t".join([str(anchorIndex), str(pairedIndex - anchorIndex - 1), str(len(self.ldMap.dVals)),str(len(self.ldMap.dVals[anchorIndex]))]) # prints intermarker counts)
+ if (pairedIndex - anchorIndex - 1) >= len(self.ldMap.dVals[anchorIndex]):
+ pRef = random.uniform(0,1)
+ if pRef > 0.5:
+@@ -166,8 +166,8 @@ class SimplePhaser:
+ altHap = temp
+
+ if pairedAllele not in [ref,alt]:
+- print "pairedAllele not ref or alt " + ref + " " + alt
+- print pairedAllele
++ print("pairedAllele not ref or alt " + ref + " " + alt)
++ print(pairedAllele)
+
+ return phasedAlleles, informativeCoords
+
+@@ -182,7 +182,7 @@ class SimplePhaser:
+ elif candidateHap[i].upper() == phasedHaps[1][i].upper():
+ currentMatch = 1
+ else:
+- print "ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i]
++ print("ERROR: " + candidateHap[i] + " does not match " + phasedHaps[0][i] + " or " + phasedHaps[1][i] + "\t" + self.ldMap.coords[i] + "\t" + self.ldMap.refs[i] + "\t" + self.ldMap.alts[i])
+ # # randomly assign match
+ # p0 = random.uniform(0,1)
+ # if p0 > 0.5:
diff --git a/haplohseq/patches/patch-src_FreqPhase.cpp b/haplohseq/patches/patch-src_FreqPhase.cpp
new file mode 100644
index 0000000000..79345c1aed
--- /dev/null
+++ b/haplohseq/patches/patch-src_FreqPhase.cpp
@@ -0,0 +1,33 @@
+$NetBSD$
+
+# Portability
+
+--- src/FreqPhase.cpp.orig 2019-11-13 14:19:06 UTC
++++ src/FreqPhase.cpp
+@@ -5,6 +5,7 @@
+ * Email: sanlucas%gmail.com@localhost
+ */
+
++#include <sysexits.h>
+ #include "FreqPhase.h"
+
+ namespace haplohseq {
+@@ -180,10 +181,17 @@ double FreqPhase::meanValue(const std::v
+ double FreqPhase::medianValue(const std::vector<double>& values) {
+ double median;
+ size_t size = values.size();
++
++ // We can probably detect this condition earlier while loading the VCF
++ if ( size == 0 ) {
++ std::cerr << "FreqPhase::medianValue(): values vector is empty." << std::endl;
++ std::cerr << "Make sure your VCF has all of GT:AD:DP in the FORMAT column." << std::endl;
++ exit(EX_DATAERR);
++ }
+ std::vector<double> tempFreqs(values);
+ sort(tempFreqs.begin(), tempFreqs.end());
+
+- if (size % 2 == 0) {
++ if (size % 2 == 0) {
+ median = (tempFreqs[size / 2 - 1] + tempFreqs[size / 2]) / 2;
+ }
+ else {
diff --git a/haplohseq/patches/patch-src_HaplohSeq.cpp b/haplohseq/patches/patch-src_HaplohSeq.cpp
new file mode 100644
index 0000000000..5548cc6617
--- /dev/null
+++ b/haplohseq/patches/patch-src_HaplohSeq.cpp
@@ -0,0 +1,24 @@
+$NetBSD$
+
+# Newer boost
+
+--- src/HaplohSeq.cpp.orig 2019-09-01 14:58:30 UTC
++++ src/HaplohSeq.cpp
+@@ -202,7 +202,7 @@ void HaplohSeq::runBafHaplohseq( std::string& obsType,
+
+ // Spawn worker threads
+ for (std::size_t t = 0; t < numThreads; t++) {
+- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
++ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
+ }
+
+ std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
+@@ -420,7 +420,7 @@ void HaplohSeq::runVcfHaplohseq( std::string& obsType,
+
+ // Spawn worker threads
+ for (std::size_t t = 0; t < numThreads; t++) {
+- threadPool.create_thread(boost::bind((unsigned long int (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
++ threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
+ }
+
+ std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
diff --git a/haplohseq/patches/patch-src_test_InputProcessorTest.cpp b/haplohseq/patches/patch-src_test_InputProcessorTest.cpp
new file mode 100644
index 0000000000..80e2483060
--- /dev/null
+++ b/haplohseq/patches/patch-src_test_InputProcessorTest.cpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Newer boost
+
+--- src/test/InputProcessorTest.cpp.orig 2019-09-01 12:33:22 UTC
++++ src/test/InputProcessorTest.cpp
+@@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE(isHetTest) {
+ BOOST_REQUIRE_EQUAL(inputProc.isHet('A','?'), false);
+ BOOST_REQUIRE_EQUAL(inputProc.isHet('A','.'), false);
+ BOOST_REQUIRE_EQUAL(inputProc.isHet('A',' '), false);
+- BOOST_REQUIRE_EQUAL(inputProc.isHet('C', NULL), true);
++ BOOST_REQUIRE_EQUAL(inputProc.isHet('C','\0'), true);
+ }
+
+ BOOST_AUTO_TEST_CASE(readAllelesTest) {
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