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1 # Makefile for ezBAMQC, utilities for the Sequence Alignment/Map format.
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2 #
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3 # Version 0.6.5
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4 #
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5 # Copyright (C) 2015 Bioinformatics Shared Resource, CSHL.
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6 # Portions copyright (C) 2015 Cold Spring Harbor Laboratory.
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7 #
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8 # Permission is hereby granted, free of charge, to any person obtaining a copy
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9 # of this software and associated documentation files (the "Software"), to deal
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10 # in the Software without restriction, including without limitation the rights
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11 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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12 # copies of the Software, and to permit persons to whom the Software is
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13 # furnished to do so, subject to the following conditions:
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14 #
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15 # The above copyright notice and this permission notice shall be included in
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16 # all copies or substantial portions of the Software.
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17 #
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18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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21 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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23 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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24 # DEALINGS IN THE SOFTWARE.
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25
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26 CC = g++
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27 CPPFLAGS = $(DFLAGS) $(INCLUDES)
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28 CFLAGS = -g -fpermissive -Wall -O9 -O3 -std=c++11 -fPIC
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29 LDFLAGS = -O9 -fpermissive
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30 LDLIBS =
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31 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
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32 LOBJS= src/ezBAMQC/GeneFeatures.o src/ezBAMQC/rRNA.o src/ezBAMQC/IntervalTree.o src/ezBAMQC/InnerDist_prof.o \
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33 src/ezBAMQC/Results.o src/ezBAMQC/Mappability.o src/ezBAMQC/Coverage_prof.o src/ezBAMQC/parseBAM.o
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34
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35 INCLUDES= -I$(HTSDIR)
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36 LIBCURSES= -lcurses # -lXCurses
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37
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38 prefix = /usr/local
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39 exec_prefix = $(prefix)
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40 bindir = $(exec_prefix)/bin
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41 mandir = $(prefix)/share/man
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42 man1dir = $(mandir)/man1
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43
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44 MKDIR_P = mkdir -p
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45 #INSTALL = install -p
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46 #INSTALL_PROGRAM = $(INSTALL)
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47 #INSTALL_DATA = $(INSTALL) -m 644
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48 #INSTALL_DIR = $(MKDIR_P) -m 755
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49
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50
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51 PROGRAMS = libBAMqc.so
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52
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53
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54 all: $(PROGRAMS)
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55
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56
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57 # Adjust $(HTSDIR) to point to your top-level htslib directory
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58 HTSDIR = ./src/htslib
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59 include $(HTSDIR)/htslib.mk
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60 HTSLIB = $(HTSDIR)/libhts.a
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61 BGZIP = $(HTSDIR)/bgzip
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62
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63
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64 PACKAGE_VERSION = 0.5
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65
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66
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67 .SUFFIXES: .cpp .o
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68
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69 .cpp.o:
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70 $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
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71
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72
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73 #lib:libbam.a
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74
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75 #libbam.a:$(LOBJS)
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76 # $(AR) -csru $@ $(LOBJS)
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77
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78 #libBAMqc.so: $(LOBJS) $(HTSLIB)
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79 # $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
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80
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81 libBAMqc.so: $(LOBJS) $(HTSLIB)
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82 # $(CC) -shared -Wl,-soname, libBAMqc.so.$(PACKAGE_VERSION) -lpthread $(LDFLAGS) -o $@ $(LOBJS) $(HTSLIB) $(LDLIBS) -lz -lm
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83 $(CC) -shared -lpthread $(LDFLAGS) -o $@ $(LOBJS) $(HTSLIB) $(LDLIBS) -lz -lm
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84 # ln -sf $@ libBAMqc.so.$(PACKAGE_VERSION)
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85
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86 Constants_h = src/ezBAMQC/Constants.h
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87 IntervalTree_h = src/ezBAMQC/IntervalTree.h $(Constants_h)
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88 GeneFeatures_h = src/ezBAMQC/GeneFeatures.h $(Constants_h)
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89 rRNA_h = src/ezBAMQC/rRNA.h $(IntervalTree_h) $(GeneFeatures_h)
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90 Results_h = src/ezBAMQC/Resualts.h
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91 Mappability_h = src/ezBAMQC/Mappability.h $(Constants_h)
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92 InnerDist_prof_h = src/ezBAMQC/InnerDist_prof.h $(GeneFeatures_h)
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93 Coverage_prof_h = src/ezBAMQC/Coverage_prof.h $(GeneFeatures_h)
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94 parseBAM_h = src/ezBAMQC/parseBAM.h
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95
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96
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97 IntervalTree.o: src/ezBAMQC/IntervalTree.cpp $(IntervalTree_h)
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98 GeneFeatures.o: src/ezBAMQC/GeneFeatures.cpp $(GeneFeatures_h)
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99 rRNA.o: src/ezBAMQC/rRNA.cpp $(rRNA_h)
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100 Results.o: src/ezBAMQC/Results.cpp $(Results_h)
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101 Mappability.o: src/ezBAMQC/Mappability.cpp $(Mappability_h) $(htslib_sam_h)
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102 InnerDist_prof.o: src/ezBAMQC/InnerDist_prof.cpp $(InnerDist_prof_h) $(htslib_sam_h)
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103 Coverage_prof.o: src/ezBAMQC/Coverage_prof.cpp $(Coverage_prof_h)
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104 parseBAM.o: src/ezBAMQC/parseBAM.cpp $(parseBAM_h) $(htslib_sam_h) $(GeneFeatures_h) $(rRNA_h) $(Mappability_h) $(Coverage_prof_h) $(InnerDist_prof_h)
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105
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106
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107 #install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
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108 # $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
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109 # $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
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110 # $(INSTALL_DATA) samtools.1 $(DESTDIR)$(man1dir)
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111
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112
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113 mostlyclean:
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114 -rm -f src/*.o
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115
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116 clean: mostlyclean
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117 -rm -f $(PROGRAMS)
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118
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119 distclean: clean
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120 -rm -f TAGS
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121
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122 clean-all: clean
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123
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124
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125 tags:
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126 ctags -f TAGS *.[ch] misc/*.[ch]
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127
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128
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129 force:
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130
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131
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132 .PHONY: all clean clean-all distclean force
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133 .PHONY: mostlyclean tags
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