debian/patches/external-htslib.patch

@@ -6,11 +6,42 @@ Description: Allow linking to external htslib
 Author: Afif Elghraoui <afif@ghraoui.name>
 Forwarded: no
 Last-Update: 2015-12-24
---- lofreq.orig/src/lofreq/Makefile.am
-+++ lofreq/src/lofreq/Makefile.am
-@@ -29,4 +29,4 @@
+Index: lofreq-2.1.3.1/src/lofreq/Makefile.am
+===================================================================
+--- lofreq-2.1.3.1.orig/src/lofreq/Makefile.am
++++ lofreq-2.1.3.1/src/lofreq/Makefile.am
+@@ -29,4 +29,4 @@ viterbi.c viterbi.h
  
  # note: order matters
  #lofreq_LDADD = @htslib_dir@/libhts.a @samtools_dir@/libbam.a
 -lofreq_LDADD = @HTSLIB@/libhts.a @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a
 +lofreq_LDADD = -L@HTSLIB@ -lhts @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a
+Index: lofreq-2.1.3.1/Makefile.am
+===================================================================
+--- lofreq-2.1.3.1.orig/Makefile.am
++++ lofreq-2.1.3.1/Makefile.am
+@@ -9,10 +9,10 @@ if ENABLE_TOOLS
+ TOOLS = src/tools
+ endif
+ 
+-LICENSES = LICENSE src/cdflib90.README src/uthash/LICENSE
++LICENSES = LICENSE src/cdflib90.README
+ EXTRA_DIST = binary_installer.sh $(LICENSES)
+ 
+-SUBDIRS = src/cdflib90 src/uthash src/lofreq src/scripts $(TOOLS) 
++SUBDIRS = src/cdflib90 src/lofreq src/scripts $(TOOLS)
+ bug-tests: all
+ 	cd tests && $(SHELL) run_all.sh;
+ 
+Index: lofreq-2.1.3.1/configure.ac
+===================================================================
+--- lofreq-2.1.3.1.orig/configure.ac
++++ lofreq-2.1.3.1/configure.ac
+@@ -215,7 +215,6 @@ AC_DEFINE([_USE_KNETFILE], [1], [KNETFIL
+ 
+ AC_CONFIG_FILES(Makefile
+         src/cdflib90/Makefile   
+-        src/uthash/Makefile
+         src/lofreq/Makefile
+         src/scripts/Makefile        
+         src/tools/setup_conf.py        

debian/upstream/metadata

 Reference:
-  Author: Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan
-  Title: "LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets"
+  Author: >
+   Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui
+   Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor
+   and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan
+  Title: >
+   LoFreq: a sequence-quality aware, ultra-sensitive variant caller
+   for uncovering cell-population heterogeneity from high-throughput
+   sequencing datasets
   Journal: Nucleic Acids Research
   Year: 2012
   Volume: 40

debian/watch

+version=4
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%lofreq-$1.tar.gz%" \
+   https://github.com/CSB5/lofreq/tags \
+   (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate