git: 51c1f17ce70a - main - biology/haplohseq: Update to 0.1.2.3
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Date: Tue, 20 May 2025 23:32:16 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=51c1f17ce70a06caaa8cfd817b6eda5bf3002af2
commit 51c1f17ce70a06caaa8cfd817b6eda5bf3002af2
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-05-20 23:28:43 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-05-20 23:28:43 +0000
biology/haplohseq: Update to 0.1.2.3
Unbreak build for boost 1.87+ (hayzam@alchemilla.io)
Switch master site to fork on Github and upstream patches
MD Anderson has ceased development and is planning a replacement
PR: 286955
Reported by: hayzam@alchemilla.io
---
biology/haplohseq/Makefile | 9 +-
biology/haplohseq/distinfo | 6 +-
biology/haplohseq/files/patch-makefile | 105 ---------------------
biology/haplohseq/files/patch-scripts_ldmap.py | 42 ---------
.../files/patch-scripts_simple__phaser.py | 31 ------
biology/haplohseq/files/patch-src_FreqPhase.cpp | 29 ------
biology/haplohseq/files/patch-src_HaplohSeq.cpp | 20 ----
.../files/patch-src_test_InputProcessorTest.cpp | 11 ---
8 files changed, 7 insertions(+), 246 deletions(-)
diff --git a/biology/haplohseq/Makefile b/biology/haplohseq/Makefile
index 8da67ec49753..128b5317242d 100644
--- a/biology/haplohseq/Makefile
+++ b/biology/haplohseq/Makefile
@@ -1,16 +1,15 @@
PORTNAME= haplohseq
-DISTVERSION= 0.1.2
-PORTREVISION= 13
+DISTVERSION= 0.1.2-3
+DISTVERSIONSUFFIX= -gfeb9267
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Identify regions of allelic imbalance
-WWW= https://sites.google.com/site/integrativecancergenomics/software/haplohseq
+WWW= https://github.com/outpaddling/haplohseq \
+ https://sites.google.com/site/integrativecancergenomics/software/haplohseq
LICENSE= MIT
-BROKEN= fails to build with Boost>=1.87
-
LIB_DEPENDS= libboost_system.so:devel/boost-libs
RUN_DEPENDS= R-cran-optparse>0:devel/R-cran-optparse
diff --git a/biology/haplohseq/distinfo b/biology/haplohseq/distinfo
index 7af7556d5596..ab9872a8d79f 100644
--- a/biology/haplohseq/distinfo
+++ b/biology/haplohseq/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1611421648
-SHA256 (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 64f61023a6795decb680c23d142b1a349988d4c0e3bef8c7d52ca33bf42f29f0
-SIZE (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 12084603
+TIMESTAMP = 1747762325
+SHA256 (outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz) = a23691f16f1c03e0dfd833896068e05eaa139d488a7094a49033aeacba948cb1
+SIZE (outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz) = 12085111
diff --git a/biology/haplohseq/files/patch-makefile b/biology/haplohseq/files/patch-makefile
deleted file mode 100644
index 5387716aa503..000000000000
--- a/biology/haplohseq/files/patch-makefile
+++ /dev/null
@@ -1,105 +0,0 @@
---- 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/biology/haplohseq/files/patch-scripts_ldmap.py b/biology/haplohseq/files/patch-scripts_ldmap.py
deleted file mode 100644
index f9fb588048b1..000000000000
--- a/biology/haplohseq/files/patch-scripts_ldmap.py
+++ /dev/null
@@ -1,42 +0,0 @@
---- 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/biology/haplohseq/files/patch-scripts_simple__phaser.py b/biology/haplohseq/files/patch-scripts_simple__phaser.py
deleted file mode 100644
index c6c5941ee00d..000000000000
--- a/biology/haplohseq/files/patch-scripts_simple__phaser.py
+++ /dev/null
@@ -1,31 +0,0 @@
---- 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/biology/haplohseq/files/patch-src_FreqPhase.cpp b/biology/haplohseq/files/patch-src_FreqPhase.cpp
deleted file mode 100644
index 9bab76aee2f5..000000000000
--- a/biology/haplohseq/files/patch-src_FreqPhase.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
---- src/FreqPhase.cpp.orig 2019-11-13 14:19:06 UTC
-+++ src/FreqPhase.cpp
-@@ -5,6 +5,7 @@
- * Email: sanlucas@gmail.com
- */
-
-+#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/biology/haplohseq/files/patch-src_HaplohSeq.cpp b/biology/haplohseq/files/patch-src_HaplohSeq.cpp
deleted file mode 100644
index a80ce577f747..000000000000
--- a/biology/haplohseq/files/patch-src_HaplohSeq.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
---- 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/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp b/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp
deleted file mode 100644
index 21ea56a8f600..000000000000
--- a/biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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) {