CMakeLists.txt

@@ -6,6 +6,9 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
 set(${PROJECT_NAME}_VERSION_MINOR 5)
 set(${PROJECT_NAME}_VERSION_PATCH 1)
 
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 set(CMAKE_CXX_FLAGS "-Wall")
 
 set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")

debian/berkeley-express-doc.examples

+sample_data/*

debian/changelog

-berkeley-express (1.5.2+dfsg-2) UNRELEASED; urgency=medium
+berkeley-express (1.5.3+dfsg-1) unstable; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Use secure copyright file specification URI.
   * Trim trailing whitespace.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Sat, 20 Oct 2018 13:12:49 +0000
+  [ Michael R. Crusoe ]
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * -doc: Include the sample data
+  * remove the version check for privacy
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 17 Nov 2019 17:17:25 +0100
 
 berkeley-express (1.5.2+dfsg-1) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libboost-thread-dev,
                libboost-system-dev,
                libboost-filesystem-dev,
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 11~),
                cmake,
                libprotobuf-dev,
                protobuf-compiler
-Standards-Version: 4.1.3
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/berkeley-express
 Vcs-Git: https://salsa.debian.org/med-team/berkeley-express.git
 Homepage: http://bio.math.berkeley.edu/eXpress/index.html

debian/patches/correct-debug-flags.patch

@@ -4,11 +4,11 @@ Description: remove forced flags and set dynamic linking
 Author: Gert Wollny <gw.fossdev@gmail.com>
 Forwarded: no 
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -6,14 +6,13 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
- set(${PROJECT_NAME}_VERSION_MINOR 5)
- set(${PROJECT_NAME}_VERSION_PATCH 1)
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -9,14 +9,13 @@
+ set(CMAKE_CXX_STANDARD 11)
+ set(CMAKE_CXX_STANDARD_REQUIRED ON)
  
 -set(CMAKE_CXX_FLAGS "-Wall")
 +#set(CMAKE_CXX_FLAGS "-Wall")
@@ -27,9 +27,9 @@ Forwarded: no
  
  find_package(Boost 1.39
      COMPONENTS
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -10,12 +10,12 @@ add_executable(express ${sources} ${head
+--- berkeley-express.orig/src/CMakeLists.txt
++++ berkeley-express/src/CMakeLists.txt
+@@ -10,12 +10,12 @@
  set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES})
  
  if (GPERFTOOLS_TCMALLOC) 

debian/patches/drop-zlib

 Description: drop unused zlib dependency
 Author: Michael R. Crusoe <crusoe@ucdavis.edu>
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -57,7 +57,6 @@ else(WIN32)
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -60,7 +60,6 @@
        message(STATUS "Do not try to find libbamtools.a")
        set(BAMTOOLS_LIBRARIES bamtools)
      endif()
@@ -10,13 +10,13 @@ Author: Michael R. Crusoe <crusoe@ucdavis.edu>
  	set(WIN32_INT 0)
  endif(WIN32)
  
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -7,7 +7,7 @@ endif(PROTOBUF_FOUND)
+--- berkeley-express.orig/src/CMakeLists.txt
++++ berkeley-express/src/CMakeLists.txt
+@@ -7,7 +7,7 @@
  
  add_executable(express ${sources} ${headers} ${PROTO_SOURCES} ${PROTO_HEADERS})
  
--set(LIBRARIES ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} ${BAMTOOLS_LIBRARIES})
+-set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES} ${ZLIB_LIBRARIES})
 +set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES})
  
  if (GPERFTOOLS_TCMALLOC) 

debian/patches/fix-bamtools-path

@@ -2,9 +2,9 @@ Author: Michael R. Crusoe <mcrusoe@msu.edu>
 Last-Update: Thu, 12 Feb 2015 09:21:09 +0100
 Description: Fix path to Debian packaged bamtools
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -33,10 +33,11 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
+--- berkeley-express.orig/CMakeLists.txt
++++ berkeley-express/CMakeLists.txt
+@@ -36,10 +36,11 @@
  
  find_package(Protobuf)
  if (PROTOBUF_FOUND)
@@ -18,7 +18,7 @@ Description: Fix path to Debian packaged bamtools
  	set(PROTO_INT 0)
  endif(PROTOBUF_FOUND)
  
-@@ -52,7 +53,9 @@ else(WIN32)
+@@ -55,7 +56,9 @@
      if (EXISTS "${PROJECT_SOURCE_DIR}/bamtools/lib/libbamtools.a")
        set(BAMTOOLS_LIBRARIES "${PROJECT_SOURCE_DIR}/bamtools/lib/libbamtools.a")
      else()
@@ -29,9 +29,9 @@ Description: Fix path to Debian packaged bamtools
      endif()
  	find_package(ZLIB REQUIRED)
  	set(WIN32_INT 0)
---- a/src/mismatchmodel.cpp
-+++ b/src/mismatchmodel.cpp
-@@ -126,7 +126,7 @@ MismatchTable::MismatchTable(string para
+--- berkeley-express.orig/src/mismatchmodel.cpp
++++ berkeley-express/src/mismatchmodel.cpp
+@@ -126,7 +126,7 @@
    size_t k = 0;
    do {
      if (k > max_indel_size) {
@@ -40,7 +40,7 @@ Description: Fix path to Debian packaged bamtools
                    "truncated at max indel length of %d.",
                    param_file_name.c_str(), max_indel_size);
        break;
-@@ -143,7 +143,7 @@ MismatchTable::MismatchTable(string para
+@@ -143,7 +143,7 @@
    k = 0;
    do {
      if (k > max_indel_size) {

debian/patches/gcc-6.patch

-Description: Fix compilation with gcc-6
-Author: Gert Wollny <gw.fossdev@gmail.com>
-Bug-Debian: https://bugs.debian.org/811859
-
---- a/src/targets.cpp
-+++ b/src/targets.cpp
-@@ -113,12 +113,12 @@
- 
-   double ll = LOG_1;
-   double tot_mass = mass(with_pseudo);
--  double tot_eff_len = cached_effective_length(lib.bias_table);
-+  double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table));
-   if (neighbors) {
-     foreach (const Target* neighbor, *neighbors) {
-       tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo));
-       tot_eff_len = log_add(tot_eff_len,
--                            neighbor->cached_effective_length(lib.bias_table));
-+                            neighbor->cached_effective_length(static_cast<bool>(lib.bias_table)));
-     }
-   }
-   ll += tot_mass - tot_eff_len;

debian/patches/privacy-breach.patch

@@ -2,8 +2,8 @@ Description: avoid privace breach JS in html doc
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
 
---- a/html/faq.html
-+++ b/html/faq.html
+--- berkeley-express.orig/html/faq.html
++++ berkeley-express/html/faq.html
 @@ -17,9 +17,6 @@
    _gaq.push(['_trackPageview']);
  
@@ -30,8 +30,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    }, true);
  </script>
  <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/index.html
-+++ b/html/index.html
+--- berkeley-express.orig/html/index.html
++++ berkeley-express/html/index.html
 @@ -17,9 +17,6 @@
    _gaq.push(['_trackPageview']);
  
@@ -58,8 +58,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    }, true);
  </script>
  <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/manual.html
-+++ b/html/manual.html
+--- berkeley-express.orig/html/manual.html
++++ berkeley-express/html/manual.html
 @@ -17,9 +17,6 @@
    _gaq.push(['_trackPageview']);
  
@@ -86,8 +86,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    }, true);
  </script>
  <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/overview.html
-+++ b/html/overview.html
+--- berkeley-express.orig/html/overview.html
++++ berkeley-express/html/overview.html
 @@ -17,9 +17,6 @@
    _gaq.push(['_trackPageview']);
  
@@ -114,8 +114,8 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    }, true);
  </script>
  <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
---- a/html/tutorial.html
-+++ b/html/tutorial.html
+--- berkeley-express.orig/html/tutorial.html
++++ berkeley-express/html/tutorial.html
 @@ -17,9 +17,6 @@
    _gaq.push(['_trackPageview']);
  
@@ -142,3 +142,152 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    }, true);
  </script>
  <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
+--- berkeley-express.orig/src/main.cpp
++++ berkeley-express/src/main.cpp
+@@ -38,10 +38,6 @@
+   #include <boost/archive/iterators/ostream_iterator.hpp>
+ #endif
+ 
+-#ifndef WIN32
+-  #include "update_check.h"
+-#endif
+-
+ using namespace std;
+ namespace po = boost::program_options;
+ namespace fs = boost::filesystem;
+@@ -365,12 +361,6 @@
+     expr_alpha_map = parse_priors(prior_file);
+   }
+ 
+-#ifndef WIN32
+-  if (!vm.count("no-update-check")) {
+-    check_version(PACKAGE_VERSION);
+-  }
+-#endif
+-
+   return 0;
+ }
+ 
+--- berkeley-express.orig/src/update_check.h
++++ /dev/null
+@@ -1,120 +0,0 @@
+-/**
+- *  update_check.h
+- *  express
+- *  Based on code from http://www.linuxhowtos.org/C_C++/socket.htm
+- *  Modified by Adam Roberts on 1/18/11.
+- */
+-
+-#include <signal.h>
+-#include <strings.h>
+-#include <sys/socket.h>
+-#include <netinet/in.h>
+-#include <netdb.h>
+-
+-int NUM_SEPS = 3;
+-int CONNECT_TIMEOUT = 5;
+-
+-static int sTimeout = 0;
+-
+-static void AlarmHandler(int sig)
+-
+-{
+-
+-	sTimeout = 1;
+-
+-}
+-
+-bool error(const char *msg)
+-{
+-	return false;
+-}
+-
+-int parse_version_str(char* version_str)
+-{
+-	int version_int = 0;
+-	char* token = strtok(version_str,".");
+-    for(int i = 0; i < NUM_SEPS; ++i)
+-    {
+-      version_int += atoi(token)*(int)pow(100.,NUM_SEPS-i);
+-	}
+-	return version_int;
+-}
+-
+-bool get_current_version(char* curr_version)
+-{
+-    int sockfd, portno, n;
+-    struct sockaddr_in serv_addr;
+-    struct hostent *server;
+-	
+-    portno = 80;
+-    sockfd = socket(AF_INET, SOCK_STREAM, 0);
+-    if (sockfd < 0)
+-
+-        return error("ERROR opening socket");
+-	
+-    server = gethostbyname("bio.math.berkeley.edu");
+-    if (server == NULL)
+-
+-        return error("ERROR, no such host");
+-
+-    bzero((char *) &serv_addr, sizeof(serv_addr));
+-    serv_addr.sin_family = AF_INET;
+-    bcopy((char *)server->h_addr,
+-
+-		  (char *)&serv_addr.sin_addr.s_addr,
+-		  server->h_length);
+-    serv_addr.sin_port = htons(portno);
+-
+-	signal(SIGALRM, AlarmHandler);
+-
+-	sTimeout = 0;
+-
+-	alarm(CONNECT_TIMEOUT);
+-
+-	
+-	int ret;
+-	ret = connect(sockfd, (struct sockaddr*)&serv_addr, sizeof(serv_addr));
+-	if (ret < 0 || sTimeout)
+-	{
+-		return error("ERROR connecting");
+-	}
+-	
+-	char buffer[1024];
+-	strcpy(buffer, "GET /eXpress/curr_xprs_version HTTP/1.1\nHost: bio.math.berkeley.edu\n\n");
+-	n = (int)write(sockfd,buffer,1024);
+-	
+-    if (n < 0)
+-
+-		return error("ERROR writing to socket");
+-	bzero(curr_version, sizeof(curr_version));
+-    n = (int)read(sockfd,buffer,1024);
+-    if (n < 0)
+-
+-		return error("ERROR reading from socket");
+-
+-	char* token;
+-	token = strtok(buffer, "$");
+-	token = strtok(NULL, "$");
+-	if (token==NULL)
+-		return error("ERROR parsing response");
+-	
+-	strcpy(curr_version, token);
+-		
+-	return true;
+-}
+-
+-void check_version(const char* this_version)
+-{
+-	char curr_version[256];
+-    memset(curr_version, 0, sizeof(curr_version));
+-	if (get_current_version(curr_version))
+-	{
+-		if (strcmp(curr_version, this_version)==0) {
+-			fprintf(stderr, "You are using eXpress v%s, which is the most recent release.\n\n", PACKAGE_VERSION);
+-		} else {
+-			fprintf(stderr, "WARNING: Your version of eXpress is not up-to-date. It is recommended that you upgrade to v%s to benefit from the most recent features and bug fixes (http://bio.math.berkeley.edu/eXpress).\n\n", curr_version);
+-    }
+-	} else {
+-		fprintf(stderr, "WARNING: Could not connect to update server to verify current version. Please check at the eXpress website (http://bio.math.berkeley.edu/eXpress).\n\n");
+-	}
+-}

debian/patches/series

 spelling-fixes
 fix-bamtools-path
 drop-zlib
-gcc-6.patch
 correct-debug-flags.patch
 privacy-breach.patch

debian/tests/control

+Tests: run-tests
+Depends: @, bowtie, samtools, gzip
+Restrictions: allow-stderr
+

debian/tests/run-tests

+#!/bin/sh -ex
+pkg=berkeley-express
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+fi
+
+cd "${AUTOPKGTEST_TMP}"
+cp /usr/share/doc/${pkg}/sample_data/* .
+gunzip *
+bowtie-build --offrate 1 transcripts.fasta transcripts
+bowtie -aS -X 800 --offrate 1 transcripts -1 reads_1.fastq -2 reads_2.fastq | samtools view -Sb - > hits.bam
+berkeley-express transcripts.fasta hits.bam

src/CMakeLists.txt

@@ -7,7 +7,7 @@ endif(PROTOBUF_FOUND)
 
 add_executable(express ${sources} ${headers} ${PROTO_SOURCES} ${PROTO_HEADERS})
 
-set(LIBRARIES ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} ${BAMTOOLS_LIBRARIES})
+set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES} ${ZLIB_LIBRARIES})
 
 if (GPERFTOOLS_TCMALLOC) 
    set(LIBRARIES ${LIBRARIES} "libtcmalloc_minimal.a")
@@ -20,7 +20,9 @@ endif(PROTOBUF_FOUND)
 
 if (WIN32)
 target_link_libraries(express ${LIBRARIES})
-else(WIN32)
+elseif(APPLE)
+target_link_libraries(express ${LIBRARIES} pthread)
+elseif(UNIX)
 target_link_libraries(express ${LIBRARIES} pthread rt)
-endif(WIN32)
+endif()
 install(TARGETS express DESTINATION bin)

src/targets.cpp

@@ -113,12 +113,12 @@ double Target::sample_likelihood(bool with_pseudo,
 
   double ll = LOG_1;
   double tot_mass = mass(with_pseudo);
-  double tot_eff_len = cached_effective_length(lib.bias_table);
+  double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table));
   if (neighbors) {
     foreach (const Target* neighbor, *neighbors) {
       tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo));
       tot_eff_len = log_add(tot_eff_len,
-                            neighbor->cached_effective_length(lib.bias_table));
+                            neighbor->cached_effective_length(static_cast<bool>(lib.bias_table)));
     }
   }
   ll += tot_mass - tot_eff_len;