.cmakelintrc

+filter=-linelength

.drone.yml.sig

-eyJhbGciOiJIUzI1NiJ9.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.-gQEOXOe_vbO3T50PByiRQSD_cEx--D-FTK3sG22AB0
\ No newline at end of file
+eyJhbGciOiJIUzI1NiJ9.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.kChHrx65f5Zt-QSX0Rb7idcN7cnZaQS9mmMDPBi3RPE
\ No newline at end of file

.drone/build.sh

@@ -12,7 +12,7 @@ cd build
 
 echo "[Drone build] cmake configuration"
 
-cmake -DDO_QUIET_MAKE=TRUE ..
+cmake -DDO_QUIET_MAKE=TRUE -DBOOST_ROOT=/usr ..
 
 echo "[Drone build] making salmon and installing locally (this could take a while)"
 

.github/ISSUE_TEMPLATE/bug_report.md

+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps and data to reproduce the behavior:
+
+Specifically, please provide at least the following information:
+
+  * Which version of salmon was used?
+  * How was salmon installed (compiled, downloaded executable, through bioconda)?
+  * Which reference (e.g. transcriptome) was used?
+  * Which read files were used?
+  * Which which program options were used?
+
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots or terminal output to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Ubuntu Linux, OSX]
+ - Version [ If you are on OSX, the output of `sw_vers`. If you are on linux the output of `uname -a` and `lsb_release -a`]
+
+**Additional context**
+Add any other context about the problem here.

.travis.yml

-#whitelist
-branches:
-    only:
-        - master
-        - develop
-
-language: cpp
-
-compiler: gcc
-
-before_install:
-    - echo "yes" | sudo apt-add-repository ppa:boost-latest
-    - echo "yes" | sudo apt-add-repository ppa:mapnik/boost-backports-1-54
-    - echo "yes" | sudo apt-add-repository ppa:h-rayflood/gcc-upper
-    - sudo apt-get clean -qq
-    - sudo apt-get update -qq
-    - sudo apt-get install -qq gcc-4.9 g++-4.9 
-    - export CC="gcc-4.9"
-    - export CXX="gcc-4.9"
-    - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50
-    - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 50
+dist: trusty
+sudo: false
+git:
+  depth: 1
+language: generic
+matrix:
+  include:
+    - env: CC=gcc-7 CXX=g++-7 AR=gcc-ar-7 NM=gcc-nm-7 RANLIB=gcc-ranlib-7
+    - env: CC=gcc-5 CXX=g++-5 AR=gcc-ar-5 NM=gcc-nm-5 RANLIB=gcc-ranlib-5
+    - language: python
+      python: "3.6"
+      name: Lint cmake files.
+      install: pip3 install cmakelint
+      script: scripts/lint.sh
+  allow_failures:
+    - name: Lint cmake files.
+  fast_finish: true
 
 install:
-    - export CXX="g++-4.9"
-    - export CC="gcc-4.9"
+  # https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test
+  - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq zlib1g-dev libbz2-dev cmake
+  - |
+    if [[ "${CC}" =~ gcc- ]]; then
+      echo "Installing ${CC}."
+      sudo apt-get install -qq "${CC}"
+    fi
+  - |
+    if [[ "${CXX}" =~ g\+\+- ]]; then
+      echo "Installing ${CXX}."
+      sudo apt-get install -qq "${CXX}"
+    fi
 
 script:
+  - LD_LIBRARY_PATH=${TRAVIS_BUILD_DIR}/lib:$LD_LIBRARY_PATH
   - mkdir build
-    - cd build 
-    - cmake -DFETCH_BOOST=TRUE -DNO_RTM=TRUE .. 
-    - travis_wait 45 make 
-    - travis_wait make install
-    - travis_wait make test VERBOSE=1
+  - pushd build
+  # Set make -j N considering Travis providing 2 cores.
+  # VERBOSE=1 to show the input commands in generatd Makefile for debug.
+  - |
+    cmake \
+      -DFETCH_BOOST=TRUE \
+      -DNO_RTM=TRUE \
+      .. && \
+    make -j 4 VERBOSE=1 && \
+    make install && \
+    ./src/salmon -h
+  - |
+    make CTEST_OUTPUT_ON_FAILURE=1 VERBOSE=1 test
+  - popd
 
 after_success:
-    - cd $TRAVIS_BUILD_DIR
   - ./scripts/push-binary.sh
 
 after_failure:
-    - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/LastTest.log
+  - echo "Failure"
+  - ls -laR $TRAVIS_BUILD_DIR/build/Testing/
+  - cat $TRAVIS_BUILD_DIR/build/Testing/Temporary/*

README.md

@@ -2,14 +2,18 @@
 [![Documentation Status](https://readthedocs.org/projects/salmon/badge/?version=latest)](http://salmon.readthedocs.org/en/latest)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/salmon/README.html)
 
+**Try out alevin (salmon's single-cell processing module)!  Get started with the [tutorial](https://combine-lab.github.io/alevin-tutorial/#blog)**
+
+**Help guide the development of Salmon, [take our survey](https://docs.google.com/forms/d/e/1FAIpQLSeWhBNE_fA_0uVHvbAlAulDmfmowv7rAYla879DZpqCARyRTQ/viewform)**
+
 What is Salmon?
 ===============
 
 Salmon is a **wicked**-fast program to produce a highly-accurate, transcript-level quantification estimates from 
-RNA-seq data.  Salmon achieves is accuracy and speed via a number of different innovations, including the 
+RNA-seq data.  Salmon achieves its accuracy and speed via a number of different innovations, including the 
 use of *quasi-mapping* (accurate but fast-to-compute proxies for traditional read alignments), and 
 massively-parallel stochastic collapsed variational inference.  The result is a versatile tool that fits nicely
-into many differnt pipelines.  For example, you can choose to make use of our *quasi-mapping* algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an **unsorted** BAM file produced with your favorite aligner), and it will use the same **wicked**-fast, state-of-the-art inference algorithm 
+into many different pipelines.  For example, you can choose to make use of our *quasi-mapping* algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an **unsorted** BAM file produced with your favorite aligner), and it will use the same **wicked**-fast, state-of-the-art inference algorithm 
 to estimate transcript-level abundances for your experiment.
 
 Give salmon a try!  You can find the latest binary releases [here](https://github.com/COMBINE-lab/salmon/releases).

cmake/Modules/FindJemalloc.cmake

@@ -28,19 +28,26 @@ find_library(JEMALLOC_LIBRARY NAMES jemalloc libjemalloc
     ${PC_JEMALLOC_LIBRARY_DIRS}
   PATH_SUFFIXES lib lib64)
 
-set(JEMALLOC_LIBRARIES ${JEMALLOC_LIBRARY})
-set(JEMALLOC_INCLUDE_DIRS ${JEMALLOC_INCLUDE_DIR})
+if(JEMALLOC_INCLUDE_DIR)
+  set(_version_regex "^#define[ \t]+JEMALLOC_VERSION[ \t]+\"([^\"]+)\".*")
+  file(STRINGS "${JEMALLOC_INCLUDE_DIR}/jemalloc/jemalloc.h"
+    JEMALLOC_VERSION REGEX "${_version_regex}")
+  string(REGEX REPLACE "${_version_regex}" "\\1"
+    JEMALLOC_VERSION "${JEMALLOC_VERSION}")
+  unset(_version_regex)
+endif()
 
-find_package_handle_standard_args(Jemalloc DEFAULT_MSG
-  JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set JEMALLOC_FOUND to TRUE
+# if all listed variables are TRUE and the requested version matches.
+find_package_handle_standard_args(Jemalloc REQUIRED_VARS
+                                  JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR
+                                  VERSION_VAR JEMALLOC_VERSION)
 
-get_property(_type CACHE JEMALLOC_ROOT PROPERTY TYPE)
-if(_type)
-  set_property(CACHE JEMALLOC_ROOT PROPERTY ADVANCED 1)
-  if("x${_type}" STREQUAL "xUNINITIALIZED")
-    set_property(CACHE JEMALLOC_ROOT PROPERTY TYPE PATH)
-  endif()
-endif()
 
-mark_as_advanced(JEMALLOC_ROOT JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)
+if(JEMALLOC_FOUND)
+  set(JEMALLOC_LIBRARIES    ${JEMALLOC_LIBRARY})
+  set(JEMALLOC_INCLUDE_DIRS ${JEMALLOC_INCLUDE_DIR})
+endif()
 
+mark_as_advanced(JEMALLOC_INCLUDE_DIR JEMALLOC_LIBRARY)

cmake/TestSalmonQuasi.cmake

+execute_process(COMMAND tar xzvf sample_data.tgz
+                WORKING_DIRECTORY ${TOPLEVEL_DIR}
+                RESULT_VARIABLE TAR_RESULT
+               )
+
+if (TAR_RESULT)
+    message(FATAL_ERROR "Error untarring sample_data.tgz")
+endif()
+
 set(SALMON_QUASI_INDEX_CMD ${CMAKE_BINARY_DIR}/salmon index -t transcripts.fasta -i sample_salmon_quasi_index --type quasi)
 execute_process(COMMAND ${SALMON_QUASI_INDEX_CMD}
                 WORKING_DIRECTORY ${TOPLEVEL_DIR}/sample_data

cmake/UnitTests.cmake

-set(TEST_COMMAND ${TOPLEVEL_DIR}/tests/unitTests)
+set(TEST_COMMAND ./unitTests)
+message(STATUS "For unit tests, will set working directory to ${TOPLEVEL_DIR}/tests")
 execute_process(COMMAND ${TEST_COMMAND} 
 	        WORKING_DIRECTORY ${TOPLEVEL_DIR}/tests
                 RESULT_VARIABLE UNIT_TEST_RESULT

current_version.txt

+VERSION_MAJOR 0
+VERSION_MINOR 12
+VERSION_PATCH 0

debian/changelog

+salmon (0.12.0+ds1-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Remove debian/gbp.conf
+  * Build-Depends: libbz2-dev, liblzma-dev
+
+ -- Andreas Tille <tille@debian.org>  Tue, 11 Dec 2018 19:29:39 +0100
+
 salmon (0.8.0+ds1-1) unstable; urgency=medium
 
   * Team upload

debian/compat

-10
+11

debian/control

@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <crusoe@ucdavis.edu>,
            Kevin Murray <spam@kdmurray.id.au>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                cmake,
                libboost-filesystem-dev,
                libboost-system-dev,
@@ -30,10 +30,13 @@ Build-Depends: debhelper (>= 10),
                python-sphinx | python3-sphinx,
                python-sphinx-rtd-theme | python3-sphinx-rtd-theme,
                zlib1g-dev,
-               libeigen3-dev
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/salmon.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/salmon.git
+               libeigen3-dev,
+               libbz2-dev,
+               liblzma-dev,
+               rapmap-dev (>= 0.12.0~)
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/salmon
+Vcs-Git: https://salsa.debian.org/med-team/salmon.git
 Homepage: https://github.com/COMBINE-lab/salmon
 
 Package: salmon

debian/gbp.conf

-[DEFAULT]
-# The default name for the upstream branch is "upstream".
-# Change it if the name is different (for instance, "master").
-upstream-branch = upstream
-# The default name for the Debian branch is "master".
-# Change it if the name is different (for instance, "debian/unstable").
-debian-branch = master
-# gbp import-orig uses the following names for the upstream tags.
-# Change the value if you are not using gbp import-orig
-upstream-tag = upstream/%(version)s
-# Always use pristine-tar.
-pristine-tar = True

debian/patches/0007-Remove-unnecessarily-linked-libraries.patch

-From: Kevin Murray <spam@kdmurray.id.au>
-Date: Sat, 30 Jan 2016 18:06:06 +0200
-Subject: Remove unnecessarily linked libraries
-
----
- CMakeLists.txt     | 2 +-
- src/CMakeLists.txt | 6 +-----
- 2 files changed, 2 insertions(+), 6 deletions(-)
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -264,7 +264,7 @@ endif()
- # Set the latest version and look for what we need
- ##
- set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59" "1.60" "1.61")
--find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer chrono program_options)
-+find_package(Boost 1.61.0 COMPONENTS iostreams filesystem system thread timer program_options)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
- message("Boost_FOUND = ${Boost_FOUND}")
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -135,9 +135,7 @@ target_link_libraries(salmon
-     jellyfish-2.0
-     bwa
-     m
--    ${LIBLZMA_LIBRARIES}
--    ${BZIP2_LIBRARIES}
--    ${TBB_LIBRARIES}
-+    tbb
-     ${LIBSALMON_LINKER_FLAGS}
-     ${NON_APPLECLANG_LIBS}
-     ${FAST_MALLOC_LIB}
-@@ -173,6 +171,7 @@ add_dependencies(salmon_core libstadenio
- add_dependencies(salmon libstadenio)
- add_dependencies(salmon_core libspdlog)
- add_dependencies(salmon libspdlog)
-+## FIXME: This was commented in version 0.7.2 in a quilt patch
- add_dependencies(salmon_core libbwa)
- add_dependencies(salmon libbwa)
- add_dependencies(salmon_core libgff)

debian/patches/0008-Remove-salmon_core-lib.patch

-From: Kevin Murray <spam@kdmurray.id.au>
-Date: Sat, 30 Jan 2016 18:06:52 +0200
-Subject: Remove salmon_core lib
-
----
- src/CMakeLists.txt | 8 ++------
- 1 file changed, 2 insertions(+), 6 deletions(-)
-
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -102,9 +102,6 @@
-   set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
- endif()
- 
--# Build the Salmon library
--add_library(salmon_core ${SALMON_LIB_SRCS} )
--
- 
- # Build the salmon executable
- add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-@@ -124,7 +121,6 @@
- 
- # Link the executable
- target_link_libraries(salmon
--    salmon_core
-     gff
-     ${PTHREAD_LIB}
-     ${Boost_LIBRARIES}
-@@ -146,42 +142,41 @@
- # External dependencies of salmon_core and salmon
- ##
- if (${FETCHED_JEMALLOC})
--   add_dependencies(salmon_core libjemalloc)
-+    #   add_dependencies(salmon_core libjemalloc)
-    add_dependencies(salmon libjemalloc)
- endif()
- 
- if (${FETCHED_BOOST})
--   add_dependencies(salmon_core libboost)
-+    # add_dependencies(salmon_core libboost)
-    add_dependencies(salmon libboost)
- endif()
- 
- if (${FETCHED_JELLYFISH})
--   add_dependencies(salmon_core libjellyfish)
-+    #add_dependencies(salmon_core libjellyfish)
-    add_dependencies(salmon libjellyfish)
- endif()
- 
- if (${FETCHED_TBB})
--   add_dependencies(salmon_core libtbb)
-+    #add_dependencies(salmon_core libtbb)
-    add_dependencies(salmon libtbb)
- endif()
- 
--add_dependencies(salmon_core libcereal)
-+#add_dependencies(salmon_core libcereal)
- add_dependencies(salmon libcereal)
--add_dependencies(salmon_core libstadenio)
-+#add_dependencies(salmon_core libstadenio)
- add_dependencies(salmon libstadenio)
--add_dependencies(salmon_core libspdlog)
-+#add_dependencies(salmon_core libspdlog)
- add_dependencies(salmon libspdlog)
- ## FIXME: This was commented in version 0.7.2 in a quilt patch
--add_dependencies(salmon_core libbwa)
-+#add_dependencies(salmon_core libbwa)
- add_dependencies(salmon libbwa)
--add_dependencies(salmon_core libgff)
-+#add_dependencies(salmon_core libgff)
- add_dependencies(salmon libgff)
--add_dependencies(salmon_core libdivsufsort)
-+#add_dependencies(salmon_core libdivsufsort)
- add_dependencies(salmon libdivsufsort)
- 
- # Link the executable
- target_link_libraries(unitTests
--    salmon_core
-     gff
-     ${PTHREAD_LIB}
-     ${Boost_LIBRARIES}
-@@ -259,7 +254,7 @@
- # install(FILES ${Boost_LIBRARIES}
- # 	           DESTINATION ${INSTALL_LIB_DIR})
- 
--install(TARGETS salmon salmon_core
-+install(TARGETS salmon
-                 RUNTIME DESTINATION bin
-                 LIBRARY DESTINATION lib
-                 ARCHIVE DESTINATION lib

debian/patches/0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch

-From: Kevin Murray <spam@kdmurray.id.au>
-Date: Sat, 30 Jan 2016 18:33:36 +0200
-Subject: Remove FIND_PACKAGE for liblzma and libbz2
-
-As these seem not to be required.
----
- CMakeLists.txt | 94 +++++++++++++++++++++++++++++-----------------------------
- 1 file changed, 47 insertions(+), 47 deletions(-)
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -209,57 +209,6 @@ if (NOT ZLIB_FOUND)
- 	message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
- endif()
- 
--find_package (LibLZMA)
--if (NOT LIBLZMA_FOUND)
--    message ("Will attempt to fetch and build liblzma")
--    message ("=======================================")
--ExternalProject_Add(liblzma
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    URL http://tukaani.org/xz/xz-5.2.2.tar.gz
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2
--    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    BUILD_IN_SOURCE TRUE
--    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
--    BUILD_COMMAND make ${QUIET_MAKE}
--    INSTALL_COMMAND make ${QUIET_MAKE} install
--)
--
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBLZMA TRUE)
--else()
--    message("Found liblzma library: ${LIBLZMA_LIBRARIES}")
--    message("===========================================")
--endif()
--
--find_package (BZip2)
--if (NOT BZIP2_FOUND)
--    message ("Will attempt to fetch and build libbz2")
--    message ("=======================================")
--ExternalProject_Add(libbz2
--    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6
--    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    BUILD_IN_SOURCE TRUE
--    CONFIGURE_COMMAND ""
--    BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
--    INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR>
--)
--# Tell cmake that the external project generated a library so we can
--# add dependencies here instead of later
--set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a)
--set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include")
--set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include")
--set (FETCHED_LIBBZ2 TRUE)
--else()
--    message("Found libbz2 library: ${BZIP2_LIBRARIES}")
--    message("===========================================")
--endif()
--
- ##
- # Set the latest version and look for what we need
- ##

debian/patches/add_MEM_F_SELF_OVLP.patch

-Description: redefine MEM_F_SELF_OVLP
- libbwa upstream has dropped MEM_F_SELF_OVLP in their commit 
- 1247dc234668c1d7357fa6343222e9b5730e832d. This patch re-introduces this
- definition to fix an FTBFS.
-Author: Sascha Steinbiss <sascha@steinbiss.name>
---- a/src/SalmonQuantify.cpp
-+++ b/src/SalmonQuantify.cpp
-@@ -54,6 +54,7 @@ extern "C" {
- #include "ksort.h"
- #include "kvec.h"
- #include "utils.h"
-+#define MEM_F_SELF_OVLP 0x40
- }
- 
- // Jellyfish 2 include
-@@ -126,6 +127,7 @@ extern "C" {
- #include "RapMapUtils.hpp"
- //#include "TextBootstrapWriter.hpp"
- 
-+
- /****** QUASI MAPPING DECLARATIONS *********/
- using MateStatus = rapmap::utils::MateStatus;
- using QuasiAlignment = rapmap::utils::QuasiAlignment;

debian/patches/cmake-typo-fixes

-Author: Michael R. Crusoe <crusoe@ucdavis.edu>
-Description: fix upstream's typos
---- a/src/SalmonQuantify.cpp
-+++ b/src/SalmonQuantify.cpp
-@@ -2277,7 +2277,7 @@ int salmonQuantify(int argc, char* argv[
-     (
-      "maxOcc,m", 
-      po::value<int>(&(memOptions->max_occ))->default_value(200),
--     "(S)MEMs occuring more than this many times won't be considered.")
-+     "(S)MEMs occurring more than this many times won't be considered.")
-     (
-      "initUniform", po::bool_switch(&(sopt.initUniform))->default_value(false),
-      "initialize the offline inference with uniform parameters, rather than seeding with online parameters.")