[med-svn] [rsem] 03/07: v1.2.27

Michael Crusoe misterc-guest at moszumanska.debian.org
Sat Mar 5 12:36:06 UTC 2016 

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch 1.2.28
in repository rsem.

commit fd85219e80de537adcccd4a38eaab25876103ba4
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Mon Feb 1 03:58:37 2016 -0800

    v1.2.27
---
 debian/changelog                |   2 +-
 debian/control                  |   3 +-
 debian/copyright                |   4 +-
 debian/patches/add-descriptions |   8 +--
 debian/patches/fix-boost        |  35 +++++--------
 debian/patches/ignore-sam       | 106 ----------------------------------------
 debian/patches/series           |   2 -
 debian/patches/spelling         |  26 +++++-----
 debian/patches/use-flags        |  95 ++++++++++++++++++-----------------
 debian/rules                    |   4 +-
 10 files changed, 90 insertions(+), 195 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 97f51f2..283ee6c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-rsem (1.2.26+dfsg-1) UNRELEASED; urgency=medium
+rsem (1.2.27+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream release
 
diff --git a/debian/control b/debian/control
index 3717946..5f5f788 100644
--- a/debian/control
+++ b/debian/control
@@ -11,7 +11,8 @@ Build-Depends: debhelper (>= 9),
                libboost-dev,
                perl,
                bowtie | bowtie2,
-               help2man
+               help2man,
+               libhts-dev
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git
 Vcs-Git: https://anonscm.debian.org/debian-med/rsem.git
diff --git a/debian/copyright b/debian/copyright
index 020b353..45fbe35 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,9 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: RSEM
 Source: http://deweylab.biostat.wisc.edu/rsem/src/
-Files-Excluded: sam boost EBSeq/*.tar.gz
+Files-Excluded: samtools-1.3/*
+                boost
+                EBSeq/*.tar.gz
 
 Files: *
 Copyright: (c) 2009-2015 Bo Li bli25 [at] berkeley [dot] edu
diff --git a/debian/patches/add-descriptions b/debian/patches/add-descriptions
index adee3cd..2fcc797 100644
--- a/debian/patches/add-descriptions
+++ b/debian/patches/add-descriptions
@@ -3,7 +3,7 @@ POD documentation
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 --- rsem.orig/convert-sam-for-rsem
 +++ rsem/convert-sam-for-rsem
-@@ -89,7 +89,7 @@
+@@ -56,7 +56,7 @@
  
  =head1 NAME
  
@@ -14,7 +14,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
 --- rsem.orig/rsem-calculate-expression
 +++ rsem/rsem-calculate-expression
-@@ -570,7 +570,7 @@
+@@ -569,7 +569,7 @@
  
  =head1 NAME
  
@@ -47,7 +47,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
 --- rsem.orig/rsem-plot-transcript-wiggles
 +++ rsem/rsem-plot-transcript-wiggles
-@@ -77,7 +77,7 @@
+@@ -81,7 +81,7 @@
  
  =head1 NAME
  
@@ -58,7 +58,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
 --- rsem.orig/rsem-prepare-reference
 +++ rsem/rsem-prepare-reference
-@@ -143,7 +143,7 @@
+@@ -158,7 +158,7 @@
  
  =head1 NAME
  
diff --git a/debian/patches/fix-boost b/debian/patches/fix-boost
index e39bbd8..29c2a7d 100644
--- a/debian/patches/fix-boost
+++ b/debian/patches/fix-boost
@@ -2,17 +2,8 @@ Description: use Debian's boost library
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 --- rsem.orig/Makefile
 +++ rsem/Makefile
-@@ -1,6 +1,6 @@
- CC = g++
--CFLAGS = -Wall -c -I.
--COFLAGS = -Wall -O3 -ffast-math -c -I.
-+CFLAGS = -Wall -c -I. -I/usr/include/
-+COFLAGS = -Wall -O3 -ffast-math -c -I. -I/usr/include
- 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
-@@ -59,8 +59,6 @@
- 	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
+@@ -70,8 +70,6 @@
+ 	$(CC) $(LFLAGS) buildReadIndex.cpp -o rsem-build-read-index
  
  
 -simul.h : boost/random.hpp
@@ -20,23 +11,23 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  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
-@@ -77,14 +75,12 @@
+@@ -88,14 +86,12 @@
  
- BamWriter.h : sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
+ BamWriter.h : $(SAMTOOLS)/sam.h $(SAMTOOLS)/bam.h sam_utils.h utils.h my_assert.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
- 	$(CC) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
+ rsem-run-em : EM.o $(SAMLIBS)
+ 	$(CC) -o rsem-run-em EM.o $(SAMLIBS) -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 simul.h sam_rsem_aux.h sampling.h boost/ra [...]
-+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 simul.h sam_rsem_aux.h sampling.h WriteRes [...]
- 	$(CC) $(COFLAGS) EM.cpp
+-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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
++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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
+ 	$(CC) $(COFLAGS) $(SAMFLAGS) EM.cpp
  
- BamConverter.h : utils.h my_assert.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
-@@ -104,14 +100,14 @@
+ bc_aux.h : $(SAMTOOLS)/bam.h
+@@ -118,14 +114,14 @@
  rsem-simulate-reads : simulation.o
  	$(CC) -o rsem-simulate-reads simulation.o
  
@@ -53,7 +44,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  	$(CC) $(COFLAGS) Gibbs.cpp
  
  Buffer.h : my_assert.h
-@@ -120,7 +116,7 @@
+@@ -134,7 +130,7 @@
  	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
  
  #some header files are omitted
@@ -61,4 +52,4 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 +calcCI.o : utils.h my_assert.h 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
  	$(CC) $(COFLAGS) calcCI.cpp
  
- rsem-get-unique : getUnique.cpp
+ rsem-get-unique : $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h getUnique.cpp $(SAMLIBS)
diff --git a/debian/patches/ignore-sam b/debian/patches/ignore-sam
index b2419ab..614723b 100644
--- a/debian/patches/ignore-sam
+++ b/debian/patches/ignore-sam
@@ -1,108 +1,2 @@
 Description: don't build local copy of samtools
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- a/Makefile
-+++ b/Makefile
-@@ -7,9 +7,6 @@
- 
- all : $(PROGRAMS)
- 
--sam/libbam.a :
--	cd sam ; ${MAKE} all
--
- Transcript.h : utils.h
- 
- Transcripts.h : utils.h my_assert.h Transcript.h
-@@ -48,13 +45,13 @@
- 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
-+SamParser.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 
-+rsem-parse-alignments : parseIt.o
-+	$(CC) -o rsem-parse-alignments parseIt.o /usr/lib/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 : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h parseIt.cpp
- 	$(CC) -Wall -O2 -c -I. parseIt.cpp
- 
- 
-@@ -76,36 +73,32 @@
- 
- HitWrapper.h : HitContainer.h
- 
--sam_rsem_aux.h : sam/bam.h
--
--sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
-+sam_rsem_cvt.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
-+BamWriter.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
-+rsem-run-em : EM.o
-+	$(CC) -o rsem-run-em EM.o /usr/lib/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 [...]
-+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 simul.h sam_rsem_aux.h sampling.h boost/ra [...]
- 	$(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
-+BamConverter.h : utils.h my_assert.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
--	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp
-+	$(CC) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
- 
--rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
--	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o bam2wig.cpp
-+	$(CC) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
- 
--rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
--	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o bam2readdepth.cpp
-+	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
- 
--wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
-+wiggle.o: wiggle.cpp wiggle.h
- 	$(CC) $(COFLAGS) wiggle.cpp
- 
- rsem-simulate-reads : simulation.o
-@@ -130,19 +123,17 @@
- 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
- 	$(CC) $(COFLAGS) calcCI.cpp
- 
--rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
--	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-get-unique : getUnique.cpp
-+	$(CC) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
- 
--rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
--	$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-sam-validator : my_assert.h samValidator.cpp
-+	$(CC) -O3 -Wall samValidator.cpp /usr/lib/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
--	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-scan-for-paired-end-reads : my_assert.h scanForPairedEndReads.cpp
-+	$(CC) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
- 
- ebseq :
- 	cd EBSeq ; ${MAKE} all
- 
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
--	cd sam ; ${MAKE} clean
--	cd EBSeq ; ${MAKE} clean
diff --git a/debian/patches/series b/debian/patches/series
index 1c402e1..71a96e4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,4 @@
 spelling
-ignore-sam
-fix-sam-includes
 fix-boost
 use-flags
 add-descriptions
diff --git a/debian/patches/spelling b/debian/patches/spelling
index 3cfe416..781c6dd 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -2,12 +2,7 @@ Author: Michael R. Crusoe
 Description: fix spelling errors
 --- rsem.orig/rsem-calculate-expression
 +++ rsem/rsem-calculate-expression
-@@ -666,11 +666,11 @@
- 
- =item B<--sampling-for-bam>
- 
--When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
-+When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
+@@ -645,7 +645,7 @@
  
  =item B<--seed> <uint32>
  
@@ -16,18 +11,27 @@ Description: fix spelling errors
  
  =item B<--single-cell-prior>
  
-@@ -776,7 +776,7 @@
+@@ -679,7 +679,7 @@
  
  =item B<--sort-bam-by-read-name>
  
--Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce determinstic maximum likelihood estimations from independet runs. Note that sorting will take long time and lots of memory. (Default: off)
-+Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce deterministic maximum likelihood estimations from independet runs. Note that sorting will take long time and lots of memory. (Default: off)
+-Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce determinstic maximum likelihood estimations from independent runs. Note that sorting will take long time and lots of memory. (Default: off)
++Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce deterministic maximum likelihood estimations from independent runs. Note that sorting will take long time and lots of memory. (Default: off)
+ 
+ =item B<--no-bam-output>
+ 
+@@ -687,7 +687,7 @@
+ 
+ =item B<--sampling-for-bam>
+ 
+-When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
++When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
  
- =item B<--sort-bam-buffer-size> <string>
+ =item B<--output-genome-bam>
  
 --- rsem.orig/README.md
 +++ rsem/README.md
-@@ -492,7 +492,7 @@
+@@ -494,7 +494,7 @@
  obtain an accurate gene-isoform relationship. Instead, RSEM provides a
  script `rsem-generate-ngvector`, which clusters transcripts based on
  measures directly relating to read mappaing ambiguity. First, it
diff --git a/debian/patches/use-flags b/debian/patches/use-flags
index 163dcd2..cc2941f 100644
--- a/debian/patches/use-flags
+++ b/debian/patches/use-flags
@@ -1,21 +1,21 @@
 Description: pass CXXFLAGS to compiler
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- a/Makefile
-+++ b/Makefile
-@@ -12,10 +12,10 @@
+--- rsem.orig/Makefile
++++ rsem/Makefile
+@@ -22,10 +22,10 @@
  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
--	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-+	$(CC) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
+-	$(CC) $(LFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts
++	$(CC) $(LFLAGS) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts
  
  rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
--	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-+	$(CC) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
+-	$(CC) $(LFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts
++	$(CC) $(LFLAGS) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts
  
  BowtieRefSeqPolicy.h : RefSeqPolicy.h
  
-@@ -25,10 +25,10 @@
+@@ -35,10 +35,10 @@
  
  
  rsem-preref : preRef.o
@@ -28,52 +28,55 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
  
  SingleRead.h : Read.h
-@@ -49,14 +49,14 @@
+@@ -60,14 +60,14 @@
  
  
- rsem-parse-alignments : parseIt.o
--	$(CC) -o rsem-parse-alignments parseIt.o /usr/lib/libbam.a -lz -lpthread 
-+	$(CC) $(LDFLAGS) -o rsem-parse-alignments parseIt.o /usr/lib/libbam.a -lz -lpthread 
+ rsem-parse-alignments : parseIt.o $(SAMLIBS)
+-	$(CC) -o rsem-parse-alignments parseIt.o $(SAMLIBS) -lz -lpthread 
++	$(CC) $(LDFLAGS) -o rsem-parse-alignments parseIt.o $(SAMLIBS) -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 parseIt.cpp
--	$(CC) -Wall -O2 -c -I. parseIt.cpp
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) -Wall -O2 -c -I. parseIt.cpp
+ parseIt.o : $(SAMTOOLS)/sam.h $(SAMTOOLS)/bam.h sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h parseIt.cpp
+-	$(CC) -Wall -O2 -c -I. $(SAMFLAGS) parseIt.cpp
++	$(CC) $(CPPFLAGS) $(CXXFLAGS) -Wall -O2 -c -I. $(SAMFLAGS) parseIt.cpp
  
  
  rsem-build-read-index : utils.h buildReadIndex.cpp
--	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
+-	$(CC) $(LFLAGS) buildReadIndex.cpp -o rsem-build-read-index
++	$(CC) $(LFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) buildReadIndex.cpp -o rsem-build-read-index
  
  
  ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
-@@ -78,55 +78,55 @@
+@@ -89,58 +89,58 @@
  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
--	$(CC) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
-+	$(CC) $(LDFLAGS) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
+ rsem-run-em : EM.o $(SAMLIBS)
+-	$(CC) -o rsem-run-em EM.o $(SAMLIBS) -lz -lpthread
++	$(CC) $(LDFLAGS) -o rsem-run-em EM.o $(SAMLIBS) -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 simul.h sam_rsem_aux.h sampling.h WriteRes [...]
--	$(CC) $(COFLAGS) EM.cpp
-+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) EM.cpp
+ 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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
+-	$(CC) $(COFLAGS) $(SAMFLAGS) EM.cpp
++	$(CC) $(CPPFLAGS) $(COFLAGS) $(SAMFLAGS) $(CXXFLAGS) EM.cpp
  
- BamConverter.h : utils.h my_assert.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
+ bc_aux.h : $(SAMTOOLS)/bam.h
  
- rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp
--	$(CC) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
+ BamConverter.h : $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h
  
- rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o bam2wig.cpp
--	$(CC) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
+ rsem-tbam2gbam : utils.h Transcripts.h Transcript.h BamConverter.h $(SAMTOOLS)/sam.h $(SAMTOOLS)/bam.h sam_utils.h my_assert.h bc_aux.h tbam2gbam.cpp $(SAMLIBS)
+-	$(CC) $(LFLAGS) $(SAMFLAGS) tbam2gbam.cpp $(SAMLIBS) -lz -lpthread -o $@
++	$(CC) $(LFLAGS) $(SAMFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) tbam2gbam.cpp $(SAMLIBS) -lz -lpthread -o $@
  
- rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o bam2readdepth.cpp
--	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
+ wiggle.o: $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h my_assert.h wiggle.h wiggle.cpp
+-	$(CC) $(COFLAGS) $(SAMFLAGS) wiggle.cpp
++	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) $(SAMFLAGS) wiggle.cpp
+ 
+ rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o $(SAMLIBS) bam2wig.cpp
+-	$(CC) $(LFLAGS) bam2wig.cpp wiggle.o $(SAMLIBS) -lz -lpthread -o $@
++	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LFLAGS) bam2wig.cpp wiggle.o $(SAMLIBS) -lz -lpthread -o $@
+ 
+ rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o $(SAMLIBS) bam2readdepth.cpp
+-	$(CC) $(LFLAGS) bam2readdepth.cpp wiggle.o $(SAMLIBS) -lz -lpthread -o $@
++	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LFLAGS) bam2readdepth.cpp wiggle.o $(SAMLIBS) -lz -lpthread -o $@
  
- wiggle.o: wiggle.cpp wiggle.h
--	$(CC) $(COFLAGS) wiggle.cpp
-+	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) wiggle.cpp
  
  rsem-simulate-reads : simulation.o
 -	$(CC) -o rsem-simulate-reads simulation.o
@@ -103,17 +106,17 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 -	$(CC) $(COFLAGS) calcCI.cpp
 +	$(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) calcCI.cpp
  
- rsem-get-unique : getUnique.cpp
--	$(CC) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
+ rsem-get-unique : $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h getUnique.cpp $(SAMLIBS)
+-	$(CC) $(LFLAGS) $(SAMFLAGS) getUnique.cpp $(SAMLIBS) -lz -lpthread -o $@
++	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LFLAGS) $(SAMFLAGS) getUnique.cpp $(SAMLIBS) -lz -lpthread -o $@
  
- rsem-sam-validator : my_assert.h samValidator.cpp
--	$(CC) -O3 -Wall samValidator.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall samValidator.cpp /usr/lib/libbam.a -lz -lpthread -o $@
+ rsem-sam-validator : $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h my_assert.h samValidator.cpp $(SAMLIBS)
+-	$(CC) $(LFLAGS) $(SAMFLAGS) samValidator.cpp $(SAMLIBS) -lz -lpthread -o $@
++	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LFLAGS) $(SAMFLAGS) samValidator.cpp $(SAMLIBS) -lz -lpthread -o $@
  
- rsem-scan-for-paired-end-reads : my_assert.h scanForPairedEndReads.cpp
--	$(CC) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
+ rsem-scan-for-paired-end-reads : $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h my_assert.h scanForPairedEndReads.cpp $(SAMLIBS)
+-	$(CC) $(LFLAGS) $(SAMFLAGS) scanForPairedEndReads.cpp $(SAMLIBS) -lz -lpthread -o $@
++	$(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LFLAGS) $(SAMFLAGS) scanForPairedEndReads.cpp $(SAMLIBS) -lz -lpthread -o $@
  
  ebseq :
  	cd EBSeq ; ${MAKE} all
diff --git a/debian/rules b/debian/rules
index 2989135..260056c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,7 @@
 #!/usr/bin/make -f
 
 DH_VERBOSE := 1
+DEB_TARGET_MULTIARCH=$(shell dpkg-architecture -qDEB_TARGET_MULTIARCH)
 
 DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
 VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
@@ -16,7 +17,8 @@ override_dh_auto_build:
 	help2man ./rsem-gff3-to-gtf --no-info --version-string="${VERSION}" \
 		--name 'Convert GFF3 files to GTF files.' > \
 		debian/rsem-gff3-to-gtf.1
-	dh_auto_build
+	dh_auto_build -- SAMLIBS="/usr/lib/libbam.a /usr/lib/${DEB_TARGET_MULTIARCH}/libhts.a" \
+		SAMTOOLS="/usr/include/samtools" SAMFLAGS="-I/usr/include"
 
 override_dh_auto_install:
 	find . -maxdepth 1 -type f -perm /u+x | xargs -n 1 -I{} dh_install {} /usr/bin/

-- 
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