gnu: rsem: Update to 1.3.1.

* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.

2 files changed, 52 insertions, 721 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67f24a6170..10330cd8b2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4800,66 +4800,79 @@ phylogenies.")
 (define-public rsem
   (package
     (name "rsem")
-    (version "1.2.20")
+    (version "1.3.1")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
-                       version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/deweylab/RSEM.git")
+             (commit (string-append "v" version))))
        (sha256
-        (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
-       (patches (search-patches "rsem-makefile.patch"))
+        (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
+       (file-name (git-file-name name version))
        (modules '((guix build utils)))
        (snippet
         '(begin
-           ;; remove bundled copy of boost
+           ;; remove bundled copy of boost and samtools
            (delete-file-recursively "boost")
+           (delete-file-recursively "samtools-1.3")
            #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
+       #:make-flags
+       (list (string-append "BOOST="
+                            (assoc-ref %build-inputs "boost")
+                            "/include/")
+             (string-append "SAMHEADERS="
+                            (assoc-ref %build-inputs "htslib")
+                            "/include/htslib/sam.h")
+             (string-append "SAMLIBS="
+                            (assoc-ref %build-inputs "htslib")
+                            "/lib/libhts.a"))
        #:phases
        (modify-phases %standard-phases
          ;; No "configure" script.
          ;; Do not build bundled samtools library.
          (replace 'configure
-                  (lambda _
-                    (substitute* "Makefile"
-                      (("^all : sam/libbam.a") "all : "))
-                    #t))
+           (lambda _
+             (substitute* "Makefile"
+               (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
+               (("^\\$\\(SAMLIBS\\).*") ""))
+             #t))
          (replace 'install
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    (let* ((out (string-append (assoc-ref outputs "out")))
-                           (bin (string-append out "/bin/"))
-                           (perl (string-append out "/lib/perl5/site_perl")))
-                      (mkdir-p bin)
-                      (mkdir-p perl)
-                      (for-each (lambda (file)
-                                  (install-file file bin))
-                                (find-files "." "rsem-.*"))
-                      (install-file "rsem_perl_utils.pm" perl))
-                    #t))
-         (add-after
-          'install 'wrap-program
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
-              (for-each (lambda (prog)
-                          (wrap-program (string-append out "/bin/" prog)
-                            `("PERL5LIB" ":" prefix
-                              (,(string-append out "/lib/perl5/site_perl")))))
-                        '("rsem-plot-transcript-wiggles"
-                          "rsem-calculate-expression"
-                          "rsem-generate-ngvector"
-                          "rsem-run-ebseq"
-                          "rsem-prepare-reference")))
-            #t)))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (string-append (assoc-ref outputs "out")))
+                    (bin (string-append out "/bin/"))
+                    (perl (string-append out "/lib/perl5/site_perl")))
+               (mkdir-p bin)
+               (mkdir-p perl)
+               (for-each (lambda (file)
+                           (install-file file bin))
+                         (find-files "." "rsem-.*"))
+               (install-file "rsem_perl_utils.pm" perl))
+             #t))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each (lambda (prog)
+                           (wrap-program (string-append out "/bin/" prog)
+                             `("PERL5LIB" ":" prefix
+                               (,(string-append out "/lib/perl5/site_perl")))))
+                         '("rsem-calculate-expression"
+                           "rsem-control-fdr"
+                           "rsem-generate-data-matrix"
+                           "rsem-generate-ngvector"
+                           "rsem-plot-transcript-wiggles"
+                           "rsem-prepare-reference"
+                           "rsem-run-ebseq"
+                           "rsem-run-prsem-testing-procedure")))
+             #t)))))
     (inputs
      `(("boost" ,boost)
-       ("ncurses" ,ncurses)
        ("r-minimal" ,r-minimal)
        ("perl" ,perl)
-       ("samtools" ,samtools-0.1)
+       ("htslib" ,htslib-1.3)
        ("zlib" ,zlib)))
     (home-page "http://deweylab.biostat.wisc.edu/rsem/")
     (synopsis "Estimate gene expression levels from RNA-Seq data")
diff --git a/gnu/packages/patches/rsem-makefile.patch b/gnu/packages/patches/rsem-makefile.patch
deleted file mode 100644
index 5481dc685f..0000000000
--- a/gnu/packages/patches/rsem-makefile.patch
+++ /dev/null
@@ -1,682 +0,0 @@
-This patch simplifies the Makefile, making it much easier to build rsem
-without the bundled version of samtools.  It has already been submitted
-upstream: https://github.com/bli25wisc/RSEM/pull/11
-
-From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 14:51:07 +0200
-Subject: [PATCH 1/7] remove all headers from Makefile
-
----
- Makefile | 95 +++++++++++-----------------------------------------------------
- 1 file changed, 16 insertions(+), 79 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 54e2603..3a55ed8 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,133 +10,70 @@ all : $(PROGRAMS)
- sam/libbam.a :
- 	cd sam ; ${MAKE} all
- 
--Transcript.h : utils.h
--
--Transcripts.h : utils.h my_assert.h Transcript.h
--
--rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
-+rsem-extract-reference-transcripts : extractRef.cpp
- 	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
- 
--rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
-+rsem-synthesis-reference-transcripts : synthesisRef.cpp
- 	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
- 
--BowtieRefSeqPolicy.h : RefSeqPolicy.h
--
--RefSeq.h : utils.h
--
--Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
--
--
- rsem-preref : preRef.o
- 	$(CC) preRef.o -o rsem-preref
- 
--preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
-+preRef.o : preRef.cpp
- 	$(CC) $(COFLAGS) preRef.cpp
- 
--
--SingleRead.h : Read.h
--
--SingleReadQ.h : Read.h
--
--PairedEndRead.h : Read.h SingleRead.h
--
--PairedEndReadQ.h : Read.h SingleReadQ.h
--
--
--PairedEndHit.h : SingleHit.h
--
--HitContainer.h : GroupInfo.h
--
--
--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
--
--
- rsem-parse-alignments : parseIt.o sam/libbam.a
- 	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread 
- 
--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
-+parseIt.o : parseIt.cpp
- 	$(CC) -Wall -O2 -c -I. parseIt.cpp
- 
--
--rsem-build-read-index : utils.h buildReadIndex.cpp
-+rsem-build-read-index : buildReadIndex.cpp
- 	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
--
--simul.h : boost/random.hpp
--
--ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
--
--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
--
--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
--
--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 
--
--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
--
--HitWrapper.h : HitContainer.h
--
--sam_rsem_aux.h : sam/bam.h
--
--sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
--
--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
--
--sampling.h : boost/random.hpp
--
--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
--
- rsem-run-em : EM.o sam/libbam.a
- 	$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
- 
--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
-+EM.o : EM.cpp
- 	$(CC) $(COFLAGS) EM.cpp
- 
--bc_aux.h : sam/bam.h
--
--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
--
--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
-+rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
- 	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
- 
--rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
-+rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
- 	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
--rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-+rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
- 	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
--wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
-+wiggle.o: wiggle.cpp
- 	$(CC) $(COFLAGS) wiggle.cpp
- 
- rsem-simulate-reads : simulation.o
- 	$(CC) -o rsem-simulate-reads simulation.o
- 
--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
-+simulation.o : simulation.cpp
- 	$(CC) $(COFLAGS) simulation.cpp
- 
- rsem-run-gibbs : Gibbs.o
- 	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
- 
--#some header files are omitted
--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 
-+Gibbs.o : Gibbs.cpp
- 	$(CC) $(COFLAGS) Gibbs.cpp
- 
--Buffer.h : my_assert.h
--
- rsem-calculate-credibility-intervals : calcCI.o
- 	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
--#some header files are omitted
--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
-+calcCI.o : calcCI.cpp
- 	$(CC) $(COFLAGS) calcCI.cpp
- 
--rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
-+rsem-get-unique : getUnique.cpp sam/libbam.a
- 	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
- 
--rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
-+rsem-sam-validator : samValidator.cpp sam/libbam.a
- 	$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
- 
--rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
-+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
- 	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
- 
- ebseq :
-
-From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:06:41 +0200
-Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default
-
----
- Makefile | 48 ++++++++++++++++++++++++------------------------
- 1 file changed, 24 insertions(+), 24 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 3a55ed8..1dd97ca 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,6 +1,6 @@
- CC = g++
--CFLAGS = -Wall -c -I.
--COFLAGS = -Wall -O3 -ffast-math -c -I.
-+CFLAGS = -Wall -I. -I./sam -I./boost
-+COFLAGS = -O3 -ffast-math -c
- 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
- 
- .PHONY : all ebseq clean
-@@ -11,70 +11,70 @@ sam/libbam.a :
- 	cd sam ; ${MAKE} all
- 
- rsem-extract-reference-transcripts : extractRef.cpp
--	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
- 
- rsem-synthesis-reference-transcripts : synthesisRef.cpp
--	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
- 
- rsem-preref : preRef.o
--	$(CC) preRef.o -o rsem-preref
-+	$(CC) $(CFLAGS) preRef.o -o rsem-preref
- 
- preRef.o : preRef.cpp
--	$(CC) $(COFLAGS) preRef.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
- 
- rsem-parse-alignments : parseIt.o sam/libbam.a
--	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread 
-+	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
- 
- parseIt.o : parseIt.cpp
--	$(CC) -Wall -O2 -c -I. parseIt.cpp
-+	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
- 
- rsem-build-read-index : buildReadIndex.cpp
--	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
-+	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
- rsem-run-em : EM.o sam/libbam.a
--	$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-+	$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
- 
- EM.o : EM.cpp
--	$(CC) $(COFLAGS) EM.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
- 
- rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
--	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
- 
- rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
--	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
- rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
--	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
- wiggle.o: wiggle.cpp
--	$(CC) $(COFLAGS) wiggle.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
- 
- rsem-simulate-reads : simulation.o
--	$(CC) -o rsem-simulate-reads simulation.o
-+	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
- 
- simulation.o : simulation.cpp
--	$(CC) $(COFLAGS) simulation.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
- 
- rsem-run-gibbs : Gibbs.o
--	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
-+	$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
- 
- Gibbs.o : Gibbs.cpp
--	$(CC) $(COFLAGS) Gibbs.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
- 
- rsem-calculate-credibility-intervals : calcCI.o
--	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-+	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
- calcCI.o : calcCI.cpp
--	$(CC) $(COFLAGS) calcCI.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
- 
- rsem-get-unique : getUnique.cpp sam/libbam.a
--	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
- 
- rsem-sam-validator : samValidator.cpp sam/libbam.a
--	$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
- 
- rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
--	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
- 
- ebseq :
- 	cd EBSeq ; ${MAKE} all
-
-From d366614ea50f79fdd93e3c76383ccb6fcdeaa8e0 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:10:49 +0200
-Subject: [PATCH 3/7] separate object rules from rules for executables
-
----
- Makefile | 50 ++++++++++++++++++++++++++------------------------
- 1 file changed, 26 insertions(+), 24 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 1dd97ca..ae4de3b 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,6 +10,32 @@ all : $(PROGRAMS)
- sam/libbam.a :
- 	cd sam ; ${MAKE} all
- 
-+ebseq :
-+	cd EBSeq ; ${MAKE} all
-+
-+
-+calcCI.o : calcCI.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
-+
-+EM.o : EM.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
-+
-+Gibbs.o : Gibbs.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
-+
-+preRef.o : preRef.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
-+
-+parseIt.o : parseIt.cpp
-+	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
-+
-+simulation.o : simulation.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
-+
-+wiggle.o: wiggle.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
-+
-+
- rsem-extract-reference-transcripts : extractRef.cpp
- 	$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
- 
-@@ -19,24 +45,15 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
- rsem-preref : preRef.o
- 	$(CC) $(CFLAGS) preRef.o -o rsem-preref
- 
--preRef.o : preRef.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
--
- rsem-parse-alignments : parseIt.o sam/libbam.a
- 	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
- 
--parseIt.o : parseIt.cpp
--	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
--
- rsem-build-read-index : buildReadIndex.cpp
- 	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
- rsem-run-em : EM.o sam/libbam.a
- 	$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
- 
--EM.o : EM.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
--
- rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
- 	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
- 
-@@ -46,27 +63,15 @@ rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
- rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
- 	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
--wiggle.o: wiggle.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
--
- rsem-simulate-reads : simulation.o
- 	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
- 
--simulation.o : simulation.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
--
- rsem-run-gibbs : Gibbs.o
- 	$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
- 
--Gibbs.o : Gibbs.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
--
- rsem-calculate-credibility-intervals : calcCI.o
- 	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
--calcCI.o : calcCI.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
--
- rsem-get-unique : getUnique.cpp sam/libbam.a
- 	$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
- 
-@@ -76,9 +81,6 @@ rsem-sam-validator : samValidator.cpp sam/libbam.a
- rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
- 	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
- 
--ebseq :
--	cd EBSeq ; ${MAKE} all
--
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
- 	cd sam ; ${MAKE} clean
-
-From 6ba1c33cccdf7c8e7df7a3189e7db204be3b1e8d Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:28:30 +0200
-Subject: [PATCH 4/7] add ./sam to library directories, link with -lbam
-
----
- Makefile | 36 ++++++++++++++++++------------------
- 1 file changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index ae4de3b..a87cc4d 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,11 +1,11 @@
- CC = g++
--CFLAGS = -Wall -I. -I./sam -I./boost
-+CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
- COFLAGS = -O3 -ffast-math -c
- 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
- 
- .PHONY : all ebseq clean
- 
--all : $(PROGRAMS)
-+all : sam/libbam.a $(PROGRAMS)
- 
- sam/libbam.a :
- 	cd sam ; ${MAKE} all
-@@ -45,23 +45,23 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
- rsem-preref : preRef.o
- 	$(CC) $(CFLAGS) preRef.o -o rsem-preref
- 
--rsem-parse-alignments : parseIt.o sam/libbam.a
--	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
-+rsem-parse-alignments : parseIt.o
-+	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
- 
- rsem-build-read-index : buildReadIndex.cpp
- 	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
--rsem-run-em : EM.o sam/libbam.a
--	$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-+rsem-run-em : EM.o
-+	$(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
- 
--rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-tbam2gbam : tbam2gbam.cpp
-+	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
- 
--rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
--	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2wig : wiggle.o bam2wig.cpp
-+	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
- 
--rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
--	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
-+	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
- 
- rsem-simulate-reads : simulation.o
- 	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
-@@ -72,14 +72,14 @@ rsem-run-gibbs : Gibbs.o
- rsem-calculate-credibility-intervals : calcCI.o
- 	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
--rsem-get-unique : getUnique.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-get-unique : getUnique.cpp
-+	$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
- 
--rsem-sam-validator : samValidator.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-sam-validator : samValidator.cpp
-+	$(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
- 
--rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
-+	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
- 
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
-
-From 5402b88c269df79ee245c1c59e15f3c8282a0220 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:33:02 +0200
-Subject: [PATCH 5/7] do not repeat target name, use $@ instead
-
----
- Makefile | 18 +++++++++---------
- 1 file changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index a87cc4d..7ec90a3 100644
---- a/Makefile
-+++ b/Makefile
-@@ -37,22 +37,22 @@ wiggle.o: wiggle.cpp
- 
- 
- rsem-extract-reference-transcripts : extractRef.cpp
--	$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
- 
- rsem-synthesis-reference-transcripts : synthesisRef.cpp
--	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
- 
- rsem-preref : preRef.o
--	$(CC) $(CFLAGS) preRef.o -o rsem-preref
-+	$(CC) $(CFLAGS) preRef.o -o $@
- 
- rsem-parse-alignments : parseIt.o
--	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
- 
- rsem-build-read-index : buildReadIndex.cpp
--	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
-+	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
- 
- rsem-run-em : EM.o
--	$(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
- 
- rsem-tbam2gbam : tbam2gbam.cpp
- 	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
-@@ -64,13 +64,13 @@ rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
- 	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
- 
- rsem-simulate-reads : simulation.o
--	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
-+	$(CC) $(CFLAGS) -o $@ simulation.o
- 
- rsem-run-gibbs : Gibbs.o
--	$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
- 
- rsem-calculate-credibility-intervals : calcCI.o
--	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
- 
- rsem-get-unique : getUnique.cpp
- 	$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
-
-From f60784bc7aa303cc825bd87dd3f5d7d26c51bded Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:44:53 +0200
-Subject: [PATCH 6/7] use automatic variables to refer to prerequisites
-
----
- Makefile | 44 ++++++++++++++++++++++----------------------
- 1 file changed, 22 insertions(+), 22 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 7ec90a3..6540d81 100644
---- a/Makefile
-+++ b/Makefile
-@@ -15,71 +15,71 @@ ebseq :
- 
- 
- calcCI.o : calcCI.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- EM.o : EM.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- Gibbs.o : Gibbs.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- preRef.o : preRef.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- parseIt.o : parseIt.cpp
--	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
-+	$(CC) $(CFLAGS) -O2 -c $<
- 
- simulation.o : simulation.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- wiggle.o: wiggle.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- 
- rsem-extract-reference-transcripts : extractRef.cpp
--	$(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
-+	$(CC) $(CFLAGS) -O3 $< -o $@
- 
- rsem-synthesis-reference-transcripts : synthesisRef.cpp
--	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
-+	$(CC) $(CFLAGS) -O3 $< -o $@
- 
- rsem-preref : preRef.o
--	$(CC) $(CFLAGS) preRef.o -o $@
-+	$(CC) $(CFLAGS) $< -o $@
- 
- rsem-parse-alignments : parseIt.o
--	$(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
- 
- rsem-build-read-index : buildReadIndex.cpp
--	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
-+	$(CC) $(CFLAGS) -O3 $< -o $@
- 
- rsem-run-em : EM.o
--	$(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
- 
- rsem-tbam2gbam : tbam2gbam.cpp
--	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- rsem-bam2wig : wiggle.o bam2wig.cpp
--	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
- 
- rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
--	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
- 
- rsem-simulate-reads : simulation.o
--	$(CC) $(CFLAGS) -o $@ simulation.o
-+	$(CC) $(CFLAGS) -o $@ $<
- 
- rsem-run-gibbs : Gibbs.o
--	$(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lpthread
- 
- rsem-calculate-credibility-intervals : calcCI.o
--	$(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lpthread
- 
- rsem-get-unique : getUnique.cpp
--	$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- rsem-sam-validator : samValidator.cpp
--	$(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
--	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
-
-From 0cf9721077f67fb4ca15fdc59cbfbf24a944debd Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:49:19 +0200
-Subject: [PATCH 7/7] split long line
-
----
- Makefile | 17 ++++++++++++++++-
- 1 file changed, 16 insertions(+), 1 deletion(-)
-
-diff --git a/Makefile b/Makefile
-index 6540d81..0ab04a5 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,22 @@
- CC = g++
- CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
- COFLAGS = -O3 -ffast-math -c
--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
-+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
- 
- .PHONY : all ebseq clean
-