gnu/packages/patches/rsem-makefile.patch

   1 This patch simplifies the Makefile, making it much easier to build rsem
   2 without the bundled version of samtools.  It has already been submitted
   3 upstream: https://github.com/bli25wisc/RSEM/pull/11
   4
   5 From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001
   6 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
   7 Date: Wed, 22 Apr 2015 14:51:07 +0200
   8 Subject: [PATCH 1/7] remove all headers from Makefile
   9
  10 ---
  11  Makefile | 95 +++++++++++-----------------------------------------------------
  12  1 file changed, 16 insertions(+), 79 deletions(-)
  13
  14 diff --git a/Makefile b/Makefile
  15 index 54e2603..3a55ed8 100644
  16 --- a/Makefile
  17 +++ b/Makefile
  18 @@ -10,133 +10,70 @@ all : $(PROGRAMS)
  19  sam/libbam.a :
  20         cd sam ; ${MAKE} all
  21
  22 -Transcript.h : utils.h
  23 -
  24 -Transcripts.h : utils.h my_assert.h Transcript.h
  25 -
  26 -rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
  27 +rsem-extract-reference-transcripts : extractRef.cpp
  28         $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
  29
  30 -rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
  31 +rsem-synthesis-reference-transcripts : synthesisRef.cpp
  32         $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
  33
  34 -BowtieRefSeqPolicy.h : RefSeqPolicy.h
  35 -
  36 -RefSeq.h : utils.h
  37 -
  38 -Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
  39 -
  40 -
  41  rsem-preref : preRef.o
  42         $(CC) preRef.o -o rsem-preref
  43
  44 -preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
  45 +preRef.o : preRef.cpp
  46         $(CC) $(COFLAGS) preRef.cpp
  47
  48 -
  49 -SingleRead.h : Read.h
  50 -
  51 -SingleReadQ.h : Read.h
  52 -
  53 -PairedEndRead.h : Read.h SingleRead.h
  54 -
  55 -PairedEndReadQ.h : Read.h SingleReadQ.h
  56 -
  57 -
  58 -PairedEndHit.h : SingleHit.h
  59 -
  60 -HitContainer.h : GroupInfo.h
  61 -
  62 -
  63 -SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
  64 -
  65 -
  66  rsem-parse-alignments : parseIt.o sam/libbam.a
  67         $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
  68
  69 -parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
  70 +parseIt.o : parseIt.cpp
  71         $(CC) -Wall -O2 -c -I. parseIt.cpp
  72
  73 -
  74 -rsem-build-read-index : utils.h buildReadIndex.cpp
  75 +rsem-build-read-index : buildReadIndex.cpp
  76         $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
  77
  78 -
  79 -simul.h : boost/random.hpp
  80 -
  81 -ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
  82 -
  83 -SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
  84 -
  85 -SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
  86 -
  87 -PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h
  88 -
  89 -PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
  90 -
  91 -HitWrapper.h : HitContainer.h
  92 -
  93 -sam_rsem_aux.h : sam/bam.h
  94 -
  95 -sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
  96 -
  97 -BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
  98 -
  99 -sampling.h : boost/random.hpp
 100 -
 101 -WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
 102 -
 103  rsem-run-em : EM.o sam/libbam.a
 104         $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
 105
 106 -EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
 107 +EM.o : EM.cpp
 108         $(CC) $(COFLAGS) EM.cpp
 109
 110 -bc_aux.h : sam/bam.h
 111 -
 112 -BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
 113 -
 114 -rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
 115 +rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
 116         $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 117
 118 -rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
 119 +rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
 120         $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 121
 122 -rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
 123 +rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
 124         $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 125
 126 -wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
 127 +wiggle.o: wiggle.cpp
 128         $(CC) $(COFLAGS) wiggle.cpp
 129
 130  rsem-simulate-reads : simulation.o
 131         $(CC) -o rsem-simulate-reads simulation.o
 132
 133 -simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp
 134 +simulation.o : simulation.cpp
 135         $(CC) $(COFLAGS) simulation.cpp
 136
 137  rsem-run-gibbs : Gibbs.o
 138         $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
 139
 140 -#some header files are omitted
 141 -Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp
 142 +Gibbs.o : Gibbs.cpp
 143         $(CC) $(COFLAGS) Gibbs.cpp
 144
 145 -Buffer.h : my_assert.h
 146 -
 147  rsem-calculate-credibility-intervals : calcCI.o
 148         $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 149
 150 -#some header files are omitted
 151 -calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
 152 +calcCI.o : calcCI.cpp
 153         $(CC) $(COFLAGS) calcCI.cpp
 154
 155 -rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
 156 +rsem-get-unique : getUnique.cpp sam/libbam.a
 157         $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
 158
 159 -rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
 160 +rsem-sam-validator : samValidator.cpp sam/libbam.a
 161         $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
 162
 163 -rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
 164 +rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
 165         $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 166
 167  ebseq :
 168
 169 From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001
 170 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 171 Date: Wed, 22 Apr 2015 15:06:41 +0200
 172 Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default
 173
 174 ---
 175  Makefile | 48 ++++++++++++++++++++++++------------------------
 176  1 file changed, 24 insertions(+), 24 deletions(-)
 177
 178 diff --git a/Makefile b/Makefile
 179 index 3a55ed8..1dd97ca 100644
 180 --- a/Makefile
 181 +++ b/Makefile
 182 @@ -1,6 +1,6 @@
 183  CC = g++
 184 -CFLAGS = -Wall -c -I.
 185 -COFLAGS = -Wall -O3 -ffast-math -c -I.
 186 +CFLAGS = -Wall -I. -I./sam -I./boost
 187 +COFLAGS = -O3 -ffast-math -c
 188  PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 189
 190  .PHONY : all ebseq clean
 191 @@ -11,70 +11,70 @@ sam/libbam.a :
 192         cd sam ; ${MAKE} all
 193
 194  rsem-extract-reference-transcripts : extractRef.cpp
 195 -       $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
 196 +       $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
 197
 198  rsem-synthesis-reference-transcripts : synthesisRef.cpp
 199 -       $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
 200 +       $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
 201
 202  rsem-preref : preRef.o
 203 -       $(CC) preRef.o -o rsem-preref
 204 +       $(CC) $(CFLAGS) preRef.o -o rsem-preref
 205
 206  preRef.o : preRef.cpp
 207 -       $(CC) $(COFLAGS) preRef.cpp
 208 +       $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
 209
 210  rsem-parse-alignments : parseIt.o sam/libbam.a
 211 -       $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
 212 +       $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
 213
 214  parseIt.o : parseIt.cpp
 215 -       $(CC) -Wall -O2 -c -I. parseIt.cpp
 216 +       $(CC) $(CFLAGS) -O2 -c parseIt.cpp
 217
 218  rsem-build-read-index : buildReadIndex.cpp
 219 -       $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
 220 +       $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
 221
 222  rsem-run-em : EM.o sam/libbam.a
 223 -       $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
 224 +       $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
 225
 226  EM.o : EM.cpp
 227 -       $(CC) $(COFLAGS) EM.cpp
 228 +       $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
 229
 230  rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
 231 -       $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 232 +       $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 233
 234  rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
 235 -       $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 236 +       $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 237
 238  rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
 239 -       $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 240 +       $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 241
 242  wiggle.o: wiggle.cpp
 243 -       $(CC) $(COFLAGS) wiggle.cpp
 244 +       $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
 245
 246  rsem-simulate-reads : simulation.o
 247 -       $(CC) -o rsem-simulate-reads simulation.o
 248 +       $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
 249
 250  simulation.o : simulation.cpp
 251 -       $(CC) $(COFLAGS) simulation.cpp
 252 +       $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
 253
 254  rsem-run-gibbs : Gibbs.o
 255 -       $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
 256 +       $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
 257
 258  Gibbs.o : Gibbs.cpp
 259 -       $(CC) $(COFLAGS) Gibbs.cpp
 260 +       $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
 261
 262  rsem-calculate-credibility-intervals : calcCI.o
 263 -       $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 264 +       $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 265
 266  calcCI.o : calcCI.cpp
 267 -       $(CC) $(COFLAGS) calcCI.cpp
 268 +       $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
 269
 270  rsem-get-unique : getUnique.cpp sam/libbam.a
 271 -       $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
 272 +       $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
 273
 274  rsem-sam-validator : samValidator.cpp sam/libbam.a
 275 -       $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
 276 +       $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
 277
 278  rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
 279 -       $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 280 +       $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 281
 282  ebseq :
 283         cd EBSeq ; ${MAKE} all
 284
 285 From d366614ea50f79fdd93e3c76383ccb6fcdeaa8e0 Mon Sep 17 00:00:00 2001
 286 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 287 Date: Wed, 22 Apr 2015 15:10:49 +0200
 288 Subject: [PATCH 3/7] separate object rules from rules for executables
 289
 290 ---
 291  Makefile | 50 ++++++++++++++++++++++++++------------------------
 292  1 file changed, 26 insertions(+), 24 deletions(-)
 293
 294 diff --git a/Makefile b/Makefile
 295 index 1dd97ca..ae4de3b 100644
 296 --- a/Makefile
 297 +++ b/Makefile
 298 @@ -10,6 +10,32 @@ all : $(PROGRAMS)
 299  sam/libbam.a :
 300         cd sam ; ${MAKE} all
 301
 302 +ebseq :
 303 +       cd EBSeq ; ${MAKE} all
 304 +
 305 +
 306 +calcCI.o : calcCI.cpp
 307 +       $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
 308 +
 309 +EM.o : EM.cpp
 310 +       $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
 311 +
 312 +Gibbs.o : Gibbs.cpp
 313 +       $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
 314 +
 315 +preRef.o : preRef.cpp
 316 +       $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
 317 +
 318 +parseIt.o : parseIt.cpp
 319 +       $(CC) $(CFLAGS) -O2 -c parseIt.cpp
 320 +
 321 +simulation.o : simulation.cpp
 322 +       $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
 323 +
 324 +wiggle.o: wiggle.cpp
 325 +       $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
 326 +
 327 +
 328  rsem-extract-reference-transcripts : extractRef.cpp
 329         $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
 330
 331 @@ -19,24 +45,15 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
 332  rsem-preref : preRef.o
 333         $(CC) $(CFLAGS) preRef.o -o rsem-preref
 334
 335 -preRef.o : preRef.cpp
 336 -       $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
 337 -
 338  rsem-parse-alignments : parseIt.o sam/libbam.a
 339         $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
 340
 341 -parseIt.o : parseIt.cpp
 342 -       $(CC) $(CFLAGS) -O2 -c parseIt.cpp
 343 -
 344  rsem-build-read-index : buildReadIndex.cpp
 345         $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
 346
 347  rsem-run-em : EM.o sam/libbam.a
 348         $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
 349
 350 -EM.o : EM.cpp
 351 -       $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
 352 -
 353  rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
 354         $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 355
 356 @@ -46,27 +63,15 @@ rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
 357  rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
 358         $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 359
 360 -wiggle.o: wiggle.cpp
 361 -       $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
 362 -
 363  rsem-simulate-reads : simulation.o
 364         $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
 365
 366 -simulation.o : simulation.cpp
 367 -       $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
 368 -
 369  rsem-run-gibbs : Gibbs.o
 370         $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
 371
 372 -Gibbs.o : Gibbs.cpp
 373 -       $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
 374 -
 375  rsem-calculate-credibility-intervals : calcCI.o
 376         $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 377
 378 -calcCI.o : calcCI.cpp
 379 -       $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
 380 -
 381  rsem-get-unique : getUnique.cpp sam/libbam.a
 382         $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
 383
 384 @@ -76,9 +81,6 @@ rsem-sam-validator : samValidator.cpp sam/libbam.a
 385  rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
 386         $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 387
 388 -ebseq :
 389 -       cd EBSeq ; ${MAKE} all
 390 -
 391  clean :
 392         rm -f *.o *~ $(PROGRAMS)
 393         cd sam ; ${MAKE} clean
 394
 395 From 6ba1c33cccdf7c8e7df7a3189e7db204be3b1e8d Mon Sep 17 00:00:00 2001
 396 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 397 Date: Wed, 22 Apr 2015 15:28:30 +0200
 398 Subject: [PATCH 4/7] add ./sam to library directories, link with -lbam
 399
 400 ---
 401  Makefile | 36 ++++++++++++++++++------------------
 402  1 file changed, 18 insertions(+), 18 deletions(-)
 403
 404 diff --git a/Makefile b/Makefile
 405 index ae4de3b..a87cc4d 100644
 406 --- a/Makefile
 407 +++ b/Makefile
 408 @@ -1,11 +1,11 @@
 409  CC = g++
 410 -CFLAGS = -Wall -I. -I./sam -I./boost
 411 +CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
 412  COFLAGS = -O3 -ffast-math -c
 413  PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 414
 415  .PHONY : all ebseq clean
 416
 417 -all : $(PROGRAMS)
 418 +all : sam/libbam.a $(PROGRAMS)
 419
 420  sam/libbam.a :
 421         cd sam ; ${MAKE} all
 422 @@ -45,23 +45,23 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
 423  rsem-preref : preRef.o
 424         $(CC) $(CFLAGS) preRef.o -o rsem-preref
 425
 426 -rsem-parse-alignments : parseIt.o sam/libbam.a
 427 -       $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
 428 +rsem-parse-alignments : parseIt.o
 429 +       $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
 430
 431  rsem-build-read-index : buildReadIndex.cpp
 432         $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
 433
 434 -rsem-run-em : EM.o sam/libbam.a
 435 -       $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
 436 +rsem-run-em : EM.o
 437 +       $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
 438
 439 -rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
 440 -       $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
 441 +rsem-tbam2gbam : tbam2gbam.cpp
 442 +       $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
 443
 444 -rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
 445 -       $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 446 +rsem-bam2wig : wiggle.o bam2wig.cpp
 447 +       $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
 448
 449 -rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
 450 -       $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
 451 +rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
 452 +       $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
 453
 454  rsem-simulate-reads : simulation.o
 455         $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
 456 @@ -72,14 +72,14 @@ rsem-run-gibbs : Gibbs.o
 457  rsem-calculate-credibility-intervals : calcCI.o
 458         $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 459
 460 -rsem-get-unique : getUnique.cpp sam/libbam.a
 461 -       $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
 462 +rsem-get-unique : getUnique.cpp
 463 +       $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
 464
 465 -rsem-sam-validator : samValidator.cpp sam/libbam.a
 466 -       $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
 467 +rsem-sam-validator : samValidator.cpp
 468 +       $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
 469
 470 -rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
 471 -       $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 472 +rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
 473 +       $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
 474
 475  clean :
 476         rm -f *.o *~ $(PROGRAMS)
 477
 478 From 5402b88c269df79ee245c1c59e15f3c8282a0220 Mon Sep 17 00:00:00 2001
 479 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 480 Date: Wed, 22 Apr 2015 15:33:02 +0200
 481 Subject: [PATCH 5/7] do not repeat target name, use $@ instead
 482
 483 ---
 484  Makefile | 18 +++++++++---------
 485  1 file changed, 9 insertions(+), 9 deletions(-)
 486
 487 diff --git a/Makefile b/Makefile
 488 index a87cc4d..7ec90a3 100644
 489 --- a/Makefile
 490 +++ b/Makefile
 491 @@ -37,22 +37,22 @@ wiggle.o: wiggle.cpp
 492
 493
 494  rsem-extract-reference-transcripts : extractRef.cpp
 495 -       $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
 496 +       $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
 497
 498  rsem-synthesis-reference-transcripts : synthesisRef.cpp
 499 -       $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
 500 +       $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
 501
 502  rsem-preref : preRef.o
 503 -       $(CC) $(CFLAGS) preRef.o -o rsem-preref
 504 +       $(CC) $(CFLAGS) preRef.o -o $@
 505
 506  rsem-parse-alignments : parseIt.o
 507 -       $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
 508 +       $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
 509
 510  rsem-build-read-index : buildReadIndex.cpp
 511 -       $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
 512 +       $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
 513
 514  rsem-run-em : EM.o
 515 -       $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
 516 +       $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
 517
 518  rsem-tbam2gbam : tbam2gbam.cpp
 519         $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
 520 @@ -64,13 +64,13 @@ rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
 521         $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
 522
 523  rsem-simulate-reads : simulation.o
 524 -       $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
 525 +       $(CC) $(CFLAGS) -o $@ simulation.o
 526
 527  rsem-run-gibbs : Gibbs.o
 528 -       $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
 529 +       $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
 530
 531  rsem-calculate-credibility-intervals : calcCI.o
 532 -       $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
 533 +       $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
 534
 535  rsem-get-unique : getUnique.cpp
 536         $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
 537
 538 From f60784bc7aa303cc825bd87dd3f5d7d26c51bded Mon Sep 17 00:00:00 2001
 539 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 540 Date: Wed, 22 Apr 2015 15:44:53 +0200
 541 Subject: [PATCH 6/7] use automatic variables to refer to prerequisites
 542
 543 ---
 544  Makefile | 44 ++++++++++++++++++++++----------------------
 545  1 file changed, 22 insertions(+), 22 deletions(-)
 546
 547 diff --git a/Makefile b/Makefile
 548 index 7ec90a3..6540d81 100644
 549 --- a/Makefile
 550 +++ b/Makefile
 551 @@ -15,71 +15,71 @@ ebseq :
 552
 553
 554  calcCI.o : calcCI.cpp
 555 -       $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
 556 +       $(CC) $(CFLAGS) $(COFLAGS) $<
 557
 558  EM.o : EM.cpp
 559 -       $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
 560 +       $(CC) $(CFLAGS) $(COFLAGS) $<
 561
 562  Gibbs.o : Gibbs.cpp
 563 -       $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
 564 +       $(CC) $(CFLAGS) $(COFLAGS) $<
 565
 566  preRef.o : preRef.cpp
 567 -       $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
 568 +       $(CC) $(CFLAGS) $(COFLAGS) $<
 569
 570  parseIt.o : parseIt.cpp
 571 -       $(CC) $(CFLAGS) -O2 -c parseIt.cpp
 572 +       $(CC) $(CFLAGS) -O2 -c $<
 573
 574  simulation.o : simulation.cpp
 575 -       $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
 576 +       $(CC) $(CFLAGS) $(COFLAGS) $<
 577
 578  wiggle.o: wiggle.cpp
 579 -       $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
 580 +       $(CC) $(CFLAGS) $(COFLAGS) $<
 581
 582
 583  rsem-extract-reference-transcripts : extractRef.cpp
 584 -       $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
 585 +       $(CC) $(CFLAGS) -O3 $< -o $@
 586
 587  rsem-synthesis-reference-transcripts : synthesisRef.cpp
 588 -       $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
 589 +       $(CC) $(CFLAGS) -O3 $< -o $@
 590
 591  rsem-preref : preRef.o
 592 -       $(CC) $(CFLAGS) preRef.o -o $@
 593 +       $(CC) $(CFLAGS) $< -o $@
 594
 595  rsem-parse-alignments : parseIt.o
 596 -       $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
 597 +       $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
 598
 599  rsem-build-read-index : buildReadIndex.cpp
 600 -       $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
 601 +       $(CC) $(CFLAGS) -O3 $< -o $@
 602
 603  rsem-run-em : EM.o
 604 -       $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
 605 +       $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
 606
 607  rsem-tbam2gbam : tbam2gbam.cpp
 608 -       $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
 609 +       $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
 610
 611  rsem-bam2wig : wiggle.o bam2wig.cpp
 612 -       $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
 613 +       $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
 614
 615  rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
 616 -       $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
 617 +       $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
 618
 619  rsem-simulate-reads : simulation.o
 620 -       $(CC) $(CFLAGS) -o $@ simulation.o
 621 +       $(CC) $(CFLAGS) -o $@ $<
 622
 623  rsem-run-gibbs : Gibbs.o
 624 -       $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
 625 +       $(CC) $(CFLAGS) -o $@ $< -lpthread
 626
 627  rsem-calculate-credibility-intervals : calcCI.o
 628 -       $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
 629 +       $(CC) $(CFLAGS) -o $@ $< -lpthread
 630
 631  rsem-get-unique : getUnique.cpp
 632 -       $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
 633 +       $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
 634
 635  rsem-sam-validator : samValidator.cpp
 636 -       $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
 637 +       $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
 638
 639  rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
 640 -       $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
 641 +       $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
 642
 643  clean :
 644         rm -f *.o *~ $(PROGRAMS)
 645
 646 From 0cf9721077f67fb4ca15fdc59cbfbf24a944debd Mon Sep 17 00:00:00 2001
 647 From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 648 Date: Wed, 22 Apr 2015 15:49:19 +0200
 649 Subject: [PATCH 7/7] split long line
 650
 651 ---
 652  Makefile | 17 ++++++++++++++++-
 653  1 file changed, 16 insertions(+), 1 deletion(-)
 654
 655 diff --git a/Makefile b/Makefile
 656 index 6540d81..0ab04a5 100644
 657 --- a/Makefile
 658 +++ b/Makefile
 659 @@ -1,7 +1,22 @@
 660  CC = g++
 661  CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
 662  COFLAGS = -O3 -ffast-math -c
 663 -PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 664 +PROGRAMS = \
 665 +  rsem-extract-reference-transcripts \
 666 +  rsem-synthesis-reference-transcripts \
 667 +  rsem-preref \
 668 +  rsem-parse-alignments \
 669 +  rsem-build-read-index \
 670 +  rsem-run-em \
 671 +  rsem-tbam2gbam \
 672 +  rsem-run-gibbs \
 673 +  rsem-calculate-credibility-intervals \
 674 +  rsem-simulate-reads \
 675 +  rsem-bam2wig \
 676 +  rsem-get-unique \
 677 +  rsem-bam2readdepth \
 678 +  rsem-sam-validator \
 679 +  rsem-scan-for-paired-end-reads
 680
 681  .PHONY : all ebseq clean
 682