diff -Nru transtermhp-2.07/analysis.cc transtermhp-2.09/analysis.cc --- transtermhp-2.07/analysis.cc 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/analysis.cc 2011-01-14 21:45:53.000000000 +0000 @@ -6,6 +6,7 @@ #include #include #include +#include #include "map-output.h" #include "conf.h" #include "seq.h" diff -Nru transtermhp-2.07/debian/changelog transtermhp-2.09/debian/changelog --- transtermhp-2.07/debian/changelog 2011-02-21 18:20:25.000000000 +0000 +++ transtermhp-2.09/debian/changelog 2011-10-28 08:47:45.000000000 +0000 @@ -1,3 +1,17 @@ +transtermhp (2.09-1) unstable; urgency=low + + [ Alex Mestiashvili ] + * New upstream release. + + [ Andreas Tille ] + * Standards-Version: 3.9.2 (no changes needed) + * Debhelper 8 (compat+control) + * Fixed Vcs fields + * Stripped citation from long descriptions because it can be found in + debian/upstream-metadata.yaml + + -- Andreas Tille Fri, 28 Oct 2011 10:44:24 +0200 + transtermhp (2.07-1) unstable; urgency=low * Initial release (Closes: #614382) diff -Nru transtermhp-2.07/debian/compat transtermhp-2.09/debian/compat --- transtermhp-2.07/debian/compat 2011-02-20 11:39:55.000000000 +0000 +++ transtermhp-2.09/debian/compat 2011-10-28 08:44:21.000000000 +0000 @@ -1 +1 @@ -7 +8 diff -Nru transtermhp-2.07/debian/control transtermhp-2.09/debian/control --- transtermhp-2.07/debian/control 2011-02-21 18:23:43.000000000 +0000 +++ transtermhp-2.09/debian/control 2011-10-28 08:46:51.000000000 +0000 @@ -3,12 +3,13 @@ Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes -Uploaders: Alex Mestiashvili -Build-Depends: debhelper (>= 7.0.50~), quilt (>= 0.47) -Standards-Version: 3.9.1 +Uploaders: Alex Mestiashvili , + Andreas Tille +Build-Depends: debhelper (>= 8), quilt (>= 0.47) +Standards-Version: 3.9.2 Homepage: http://transterm.cbcb.umd.edu/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/transtermhp/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/transtermhp/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/transtermhp/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/transtermhp/trunk/ Package: transtermhp Architecture: any @@ -17,16 +18,5 @@ TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true - terminator. TransTermHP is described in: - . - C. Kingsford, K. Ayanbule and S.L. Salzberg. Rapid, accurate, - computational discovery of Rho-independent transcription terminators - illuminates their relationship to DNA uptake. Genome Biology 8:R22 - (2007). - . - A predecessor system, TransTerm, that used very different search and - scoring algorithms is described in: - . - Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and - Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial - Genomes. J Mol Biol 301, (1), 27-33 (2000) + terminator. TransTermHP is the successor of TransTerm which was using + very different search and scoring algorithms. diff -Nru transtermhp-2.07/debian/copyright transtermhp-2.09/debian/copyright --- transtermhp-2.07/debian/copyright 2011-02-20 11:39:55.000000000 +0000 +++ transtermhp-2.09/debian/copyright 2011-03-01 13:40:22.000000000 +0000 @@ -3,7 +3,7 @@ Source: http://transterm.cbcb.umd.edu/index.php Files: * -Copyright: Steven Salzberg salzberg@umiacs.umd.edu +Copyright: Carl Kingsford carlk@umiacs.umd.edu License: GPL-2.0+ Files: 2ndscore.cc diff -Nru transtermhp-2.07/debian/patches/missing_headers transtermhp-2.09/debian/patches/missing_headers --- transtermhp-2.07/debian/patches/missing_headers 2011-02-20 11:39:55.000000000 +0000 +++ transtermhp-2.09/debian/patches/missing_headers 1970-01-01 00:00:00.000000000 +0000 @@ -1,46 +0,0 @@ -Description: fixed missing headers in the source . -Author: Alex Mestiashvili -Last-Update: 2011-02-19 ---- transtermhp-2.0.7.orig/seq.cc -+++ transtermhp-2.0.7/seq.cc -@@ -5,6 +5,10 @@ - #include - #include - #include -+#include -+#include -+#include -+#include - - #include "seq.h" - #include "util.h" ---- transtermhp-2.0.7.orig/seq.h -+++ transtermhp-2.0.7/seq.h -@@ -4,6 +4,7 @@ - #ifndef SEQ_H - #define SEQ_H - #include -+#include - #include - #include - ---- transtermhp-2.0.7.orig/search.cc -+++ transtermhp-2.0.7/search.cc -@@ -10,6 +10,7 @@ - #include "seq.h" - #include "ermolaeva-score.h" - #include "util.h" -+#include - - int UWINDOW_SIZE = 6; - int UWINDOW_REQUIRE = 3; ---- transtermhp-2.0.7.orig/analysis.cc -+++ transtermhp-2.0.7/analysis.cc -@@ -6,6 +6,7 @@ - #include - #include - #include -+#include - #include "map-output.h" - #include "conf.h" - #include "seq.h" diff -Nru transtermhp-2.07/debian/patches/series transtermhp-2.09/debian/patches/series --- transtermhp-2.07/debian/patches/series 2011-02-20 11:39:55.000000000 +0000 +++ transtermhp-2.09/debian/patches/series 1970-01-01 00:00:00.000000000 +0000 @@ -1 +0,0 @@ -missing_headers diff -Nru transtermhp-2.07/debian/rules transtermhp-2.09/debian/rules --- transtermhp-2.07/debian/rules 2011-02-22 13:18:47.000000000 +0000 +++ transtermhp-2.09/debian/rules 2011-03-01 13:40:22.000000000 +0000 @@ -16,5 +16,8 @@ # don't forget to notify upstream. override_dh_auto_test: +override_dh_installchangelogs: + dh_installchangelogs RELEASE-NOTES.txt + get-orig-source: . debian/get-orig-source diff -Nru transtermhp-2.07/ermolaeva-score.h transtermhp-2.09/ermolaeva-score.h --- transtermhp-2.07/ermolaeva-score.h 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/ermolaeva-score.h 2011-01-14 21:45:53.000000000 +0000 @@ -86,9 +86,9 @@ Energy forward_pair(char ch1, char ch2) { - if(ch1 == 'G' && ch2 == 'C' || ch1 == 'C' && ch2 == 'G') return GC; - if(ch1 == 'T' && ch2 == 'A' || ch1 == 'A' && ch2 == 'T') return AU; - if(ch1 == 'T' && ch2 == 'G' || ch1 == 'G' && ch2 == 'T') return GU; + if((ch1 == 'G' && ch2 == 'C') || (ch1 == 'C' && ch2 == 'G')) return GC; + if((ch1 == 'T' && ch2 == 'A') || (ch1 == 'A' && ch2 == 'T')) return AU; + if((ch1 == 'T' && ch2 == 'G') || (ch1 == 'G' && ch2 == 'T')) return GU; if(ch1 == PADDING_CHAR || ch2 == PADDING_CHAR) return 1000.0; return MM; } @@ -99,9 +99,9 @@ Energy reverse_pair(char ch1, char ch2) { - if(ch1 == 'G' && ch2 == 'C' || ch1 == 'C' && ch2 == 'G') return GC; - if(ch1 == 'T' && ch2 == 'A' || ch1 == 'A' && ch2 == 'T') return AU; - if(ch1 == 'A' && ch2 == 'C' || ch1 == 'C' && ch2 == 'A') return GU; + if((ch1 == 'G' && ch2 == 'C') || (ch1 == 'C' && ch2 == 'G')) return GC; + if((ch1 == 'T' && ch2 == 'A') || (ch1 == 'A' && ch2 == 'T')) return AU; + if((ch1 == 'A' && ch2 == 'C') || (ch1 == 'C' && ch2 == 'A')) return GU; if(ch1 == PADDING_CHAR || ch2 == PADDING_CHAR) return 1000.0; return MM; } diff -Nru transtermhp-2.07/Makefile transtermhp-2.09/Makefile --- transtermhp-2.07/Makefile 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/Makefile 2011-01-14 21:45:53.000000000 +0000 @@ -4,7 +4,7 @@ # "make clean" removes all results of the compilation # "make no_obj" removes all the .o files -VER=2.07 +VER=2.09 # files used for the main transterm program OBJ = seq.o \ diff -Nru transtermhp-2.07/search.cc transtermhp-2.09/search.cc --- transtermhp-2.07/search.cc 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/search.cc 2011-01-14 21:45:53.000000000 +0000 @@ -6,6 +6,7 @@ #include #include #include +#include #include "transterm.h" #include "seq.h" #include "ermolaeva-score.h" @@ -52,11 +53,11 @@ bool check_tail(char letter, SeqPtr cp) { - return cp[0] == letter && cp[1] == letter && cp[2] == letter || - cp[1] == letter && cp[2] == letter && cp[3] == letter || - cp[2] == letter && cp[3] == letter && cp[4] == letter || - cp[3] == letter && cp[4] == letter && cp[5] == letter || - cp[4] == letter && cp[5] == letter && cp[6] == letter; + return (cp[0] == letter && cp[1] == letter && cp[2] == letter) || + (cp[1] == letter && cp[2] == letter && cp[3] == letter) || + (cp[2] == letter && cp[3] == letter && cp[4] == letter) || + (cp[3] == letter && cp[4] == letter && cp[5] == letter) || + (cp[4] == letter && cp[5] == letter && cp[6] == letter); } diff -Nru transtermhp-2.07/seq.cc transtermhp-2.09/seq.cc --- transtermhp-2.07/seq.cc 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/seq.cc 2011-01-14 21:45:53.000000000 +0000 @@ -5,9 +5,10 @@ #include #include #include +#include -#include "seq.h" #include "util.h" +#include "seq.h" const size_t INIT_SEQ_ALLOC = 1000000; diff -Nru transtermhp-2.07/seq.h transtermhp-2.09/seq.h --- transtermhp-2.07/seq.h 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/seq.h 2011-01-14 21:45:53.000000000 +0000 @@ -6,6 +6,9 @@ #include #include #include +#include +#include +#include using namespace std; diff -Nru transtermhp-2.07/transterm.cc transtermhp-2.09/transterm.cc --- transtermhp-2.07/transterm.cc 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/transterm.cc 2011-01-14 21:45:53.000000000 +0000 @@ -251,7 +251,7 @@ int main(int argc, char * argv[]) { - cout << "TransTermHP v2.07 (built on " << __DATE__ << ")" << endl; + cout << "TransTermHP v2.08 (built on " << __DATE__ << ")" << endl; time_t start_time = time(NULL); // read commandline options diff -Nru transtermhp-2.07/util.h transtermhp-2.09/util.h --- transtermhp-2.07/util.h 2009-01-21 18:54:40.000000000 +0000 +++ transtermhp-2.09/util.h 2011-01-14 21:45:53.000000000 +0000 @@ -7,6 +7,7 @@ #include #include #include +#include using namespace std;