pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
haplohseq: Upstream most patches
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Sat Jan 23 19:10:15 2021 -0600
Changeset: 53326eba0bf92fa39c3f974b6255d12122717d32
Modified Files:
haplohseq/Makefile
haplohseq/distinfo
Removed Files:
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: Upstream most patches
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=53326eba0bf92fa39c3f974b6255d12122717d32
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
haplohseq/Makefile | 11 +--
haplohseq/distinfo | 14 +--
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 ---
9 files changed, 9 insertions(+), 288 deletions(-)
diffs:
diff --git a/haplohseq/Makefile b/haplohseq/Makefile
index 53ba9d87f8..98640d74c7 100644
--- a/haplohseq/Makefile
+++ b/haplohseq/Makefile
@@ -1,21 +1,20 @@
# $NetBSD$
-DISTNAME= haplohseq-0.1.2
+DISTNAME= haplohseq-0.1.2.2
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
GITHUB_PROJECT= haplohseq
+GITHUB_TAG= e4892945eced075a5bb98f208786cdf85eb3d82a
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://sites.google.com/site/integrativecancergenomics/software/haplohseq
COMMENT= Identify regions of allelic imbalance
LICENSE= mit
-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; ${PYTHONBIN}|'
+SUBST_SED.test+= -e 's|python|${PYTHONBIN}|'
SUBST_FILES.test= example/example_run.sh
USE_LANGUAGES= c c++
@@ -32,10 +31,10 @@ post-patch:
post-install:
${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${DESTDIR}${PREFIX}/bin
- (cd ${WRKSRC} && ${RM} scripts/*.orig && pax -rw example ldmap scripts ${DESTDIR}${EXAMPLESDIR})
+ (cd ${WRKSRC} && pax -rw example ldmap scripts ${DESTDIR}${EXAMPLESDIR})
do-test:
- (cd ${WRKSRC}/build/test && ${SH} ${FILESDIR}/run-tests)
+ (cd ${WRKSRC}/build/test && ${SH} ${WRKSRC}/src/test/run-tests)
.include "../../devel/boost-libs/buildlink3.mk"
.include "../../lang/python/application.mk"
diff --git a/haplohseq/distinfo b/haplohseq/distinfo
index 2ba38bf958..3453c57605 100644
--- a/haplohseq/distinfo
+++ b/haplohseq/distinfo
@@ -1,12 +1,6 @@
$NetBSD$
-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
+SHA1 (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 0aa74b0045bb122dbacb5d20248a2f4b42f4cf8e
+RMD160 (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 5fe4b210c3ef7a0cdc88463e39e4766c30215191
+SHA512 (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 8de2c75d4e443eab79f520d43bd2e0c238dca798bf53cc7821d6fe8bdf94f3d3ae3b9319b9b21aae10dab6b52e5c1e81380380c456a240bfcfa8863b83c5feff
+Size (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 12085199 bytes
diff --git a/haplohseq/files/run-tests b/haplohseq/files/run-tests
deleted file mode 100644
index 1ecc6ebc5e..0000000000
--- a/haplohseq/files/run-tests
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/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
deleted file mode 100644
index d7d1bdfc19..0000000000
--- a/haplohseq/patches/patch-makefile
+++ /dev/null
@@ -1,109 +0,0 @@
-$NetBSD$
-
-# 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) $(LDFLAGS)
- ############################## END TEST LOGIC ##############################
-
-
diff --git a/haplohseq/patches/patch-scripts_ldmap.py b/haplohseq/patches/patch-scripts_ldmap.py
deleted file mode 100644
index e868ab6704..0000000000
--- a/haplohseq/patches/patch-scripts_ldmap.py
+++ /dev/null
@@ -1,46 +0,0 @@
-$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
deleted file mode 100644
index 1aa33ee892..0000000000
--- a/haplohseq/patches/patch-scripts_simple__phaser.py
+++ /dev/null
@@ -1,35 +0,0 @@
-$NetBSD$
-
-# 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
deleted file mode 100644
index 79345c1aed..0000000000
--- a/haplohseq/patches/patch-src_FreqPhase.cpp
+++ /dev/null
@@ -1,33 +0,0 @@
-$NetBSD$
-
-# 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
deleted file mode 100644
index 5548cc6617..0000000000
--- a/haplohseq/patches/patch-src_HaplohSeq.cpp
+++ /dev/null
@@ -1,24 +0,0 @@
-$NetBSD$
-
-# 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
deleted file mode 100644
index 80e2483060..0000000000
--- a/haplohseq/patches/patch-src_test_InputProcessorTest.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# 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) {
Home |
Main Index |
Thread Index |
Old Index