From bf55cd562402ce01dea0c19dc6783f6322047070 Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell
Date: Wed, 10 Feb 2016 11:18:29 +0100
Subject: [PATCH 01/26] [FIX] build warnings
---
apps/yara/bits_matches.h | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/apps/yara/bits_matches.h b/apps/yara/bits_matches.h
index 3e1e901784..7baeb85d3c 100644
--- a/apps/yara/bits_matches.h
+++ b/apps/yara/bits_matches.h
@@ -836,8 +836,10 @@ findProperMates(TMatches const & mates, TMatch const & match,
mateLeq.errors = 0;
mateGeq.errors = MemberLimits::VALUE;
- TReadSeqSize deltaMinus = _max((TSignedSize)0, (TSignedSize)mean - 6 * stdDev - (TSignedSize)mateLength);
- TReadSeqSize deltaPlus = _max((TSignedSize)0, (TSignedSize)mean + 6 * stdDev - (TSignedSize)mateLength);
+ TReadSeqSize deltaMinus = std::max(static_cast(0),
+ static_cast(mean - 6 * stdDev - mateLength));
+ TReadSeqSize deltaPlus = std::max(static_cast(0),
+ static_cast(mean + 6 * stdDev - mateLength));
// --> ... mate
if (onForwardStrand(match))
From 2d4c5949b0b4f3c4ba20bd8cf47749e00e596edb Mon Sep 17 00:00:00 2001
From: marehr
Date: Wed, 10 Feb 2016 13:50:08 +0100
Subject: [PATCH 02/26] [INTERNAL] sequenceId in fragment.h shouldn't use
const_cast
---
include/seqan/align/fragment.h | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/include/seqan/align/fragment.h b/include/seqan/align/fragment.h
index dcdb6ac1e3..1db7f7ba0f 100644
--- a/include/seqan/align/fragment.h
+++ b/include/seqan/align/fragment.h
@@ -341,12 +341,20 @@ label(Fragment const& f,
template
inline typename Id >::Type &
-sequenceId(Fragment const& f,
+sequenceId(Fragment & f,
TVal const seqId)
{
SEQAN_CHECKPOINT
- typedef typename Id >::Type TId;
- return ((TId) seqId == 0) ? const_cast(f.seqId1) : const_cast(f.seqId2);
+ return (seqId == (TVal)0) ? f.seqId1 : f.seqId2;
+}
+
+template
+inline typename Id >::Type const &
+sequenceId(Fragment const & f,
+ TVal const seqId)
+{
+ SEQAN_CHECKPOINT
+ return (seqId == (TVal)0) ? f.seqId1 : f.seqId2;
}
//////////////////////////////////////////////////////////////////////////////
From 622f5a7ebea17d690e9d6b8ca75f7a1c7c421f57 Mon Sep 17 00:00:00 2001
From: marehr
Date: Wed, 10 Feb 2016 14:00:24 +0100
Subject: [PATCH 03/26] [INTERNAL] idToPosition correct return type
---
include/seqan/sequence/string_set_dependent_tight.h | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/include/seqan/sequence/string_set_dependent_tight.h b/include/seqan/sequence/string_set_dependent_tight.h
index 0e2b0ea120..3314c9f31f 100644
--- a/include/seqan/sequence/string_set_dependent_tight.h
+++ b/include/seqan/sequence/string_set_dependent_tight.h
@@ -319,7 +319,7 @@ positionToId(StringSet > const & me,
// --------------------------------------------------------------------------
template
-inline typename Id > >::Type
+inline typename Position > >::Type
idToPosition(StringSet > const & me,
TId const id)
{
From c1dcef79d73f8a1dbf757f8ac2b68fac35786a74 Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell
Date: Wed, 10 Feb 2016 16:17:05 +0100
Subject: [PATCH 04/26] fix static build on non DEVELOP target and make
optional for DEVELOP target
---
util/cmake/SeqAnBuildSystem.cmake | 59 ++++++++++++++++++++-----------
1 file changed, 38 insertions(+), 21 deletions(-)
diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
index 7a56c27aa7..1fb4df4dab 100644
--- a/util/cmake/SeqAnBuildSystem.cmake
+++ b/util/cmake/SeqAnBuildSystem.cmake
@@ -126,12 +126,12 @@ endfunction (add_executable)
# Macro seqan_add_app_subdirectory (APP_NAME)
# ---------------------------------------------------------------------------
-macro (seqan_add_app_subdirectory APP_NAME)
- if (("${SEQAN_BUILD_SYSTEM}" STREQUAL "SEQAN_RELEASE") OR
- "${SEQAN_BUILD_SYSTEM}" STREQUAL "APP:${APP_NAME}")
- add_subdirectory (${APP_NAME})
- endif ()
-endmacro (seqan_add_app_subdirectory)
+# macro (seqan_add_app_subdirectory APP_NAME)
+# if (("${SEQAN_BUILD_SYSTEM}" STREQUAL "SEQAN_RELEASE") OR
+# "${SEQAN_BUILD_SYSTEM}" STREQUAL "APP:${APP_NAME}")
+# add_subdirectory (${APP_NAME})
+# endif ()
+# endmacro (seqan_add_app_subdirectory)
# ---------------------------------------------------------------------------
# Macro seqan_register_apps ()
@@ -148,23 +148,35 @@ macro (seqan_register_apps)
set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
# enable static linkage for seqan apps
- if (NOT CMAKE_SYSTEM_NAME MATCHES "Windows")
+ if (SEQAN_STATIC_APPS AND (NOT CMAKE_SYSTEM_NAME MATCHES "Windows"))
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
- # libstdc++ is being used and needs be explicitly "statified"
- if (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_SYSTEM_NAME MATCHES "Linux")
- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++")
- endif (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_SYSTEM_NAME MATCHES "Linux")
- # if not apple make other libs static (apple does not support static builds except for the above)
- if (NOT APPLE)
+ if (APPLE)
+ # static build not supported on apple, but at least we can include gcc libs
+ if (CMAKE_COMPILER_IS_GNUCXX)
+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+ endif (CMAKE_COMPILER_IS_GNUCXX)
+ else (APPLE)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
- endif (NOT APPLE)
- # on linux cmake adds -rdynamic automatically which clang can't handle in static builds
- if (CMAKE_SYSTEM_NAME MATCHES "Linux")
- SET(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "")
- endif (CMAKE_SYSTEM_NAME MATCHES "Linux")
- # not that these checks are more than OS, because we have many possible combinations between
- # OS, compiler and STL used
- endif (NOT CMAKE_SYSTEM_NAME MATCHES "Windows")
+
+ # make sure -Wl,-Bdynamic isn't added automatically
+ set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS)
+ # make sure -fPIC isn't added automatically
+ set(CMAKE_SHARED_LIBRARY_CXX_FLAGS)
+
+ # for ENTIRELY UNKOWN reasons find_package returns libs for static
+ # linking (.a) when building as SEQAN_RELEASE_APPS or APP:* but
+ # .so when building DEVELOP. In the latter case it also encloses the
+ # static libs with -Bdynamic which turns static off for system libs.
+ # Here we remove these (so statics works), but only for NON-DEVELOP
+ # on non-linux.
+
+ # this one must not be unset on FreeBSD if not building APPs individually
+ if ((CMAKE_SYSTEM_NAME MATCHES "Linux") OR (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP"))
+ # make sure -rdynamic isn't added automatically
+ set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
+ endif ((CMAKE_SYSTEM_NAME MATCHES "Linux") OR (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP"))
+ endif (APPLE)
+ endif (SEQAN_STATIC_APPS AND (NOT CMAKE_SYSTEM_NAME MATCHES "Windows"))
# Enable global exception handler for all seqan apps.
set (SEQAN_DEFINITIONS "${SEQAN_DEFINITIONS} -DSEQAN_GLOBAL_EXCEPTION_HANDLER")
@@ -222,6 +234,11 @@ macro (seqan_build_system_init)
endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
endif ()
+ if (("${SEQAN_BUILD_SYSTEM}" MATCHES "SEQAN_RELEASE") OR
+ ("${SEQAN_BUILD_SYSTEM}" MATCHES "APP"))
+ set (SEQAN_STATIC_APPS TRUE CACHE INTERNAL "Create static app binaries")
+ endif ()
+
set (SEQAN_BUILD_SYSTEM "DEVELOP" CACHE STRING "Build/Release mode to select. One of DEVELOP SEQAN_RELEASE, APP:\${APP_NAME}. Defaults to DEVELOP.")
set (_CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/include")
From ef178493da29e8c3f4c39ba0de14ab5dc880b390 Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell
Date: Wed, 10 Feb 2016 16:36:54 +0100
Subject: [PATCH 05/26] [fix] siwtch two of the flags; behaviour unrelated to
linux/freebsd
---
util/cmake/SeqAnBuildSystem.cmake | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
index 1fb4df4dab..1bbd86c698 100644
--- a/util/cmake/SeqAnBuildSystem.cmake
+++ b/util/cmake/SeqAnBuildSystem.cmake
@@ -158,7 +158,7 @@ macro (seqan_register_apps)
else (APPLE)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
- # make sure -Wl,-Bdynamic isn't added automatically
+ # make sure -rdynamic isn't added automatically
set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS)
# make sure -fPIC isn't added automatically
set(CMAKE_SHARED_LIBRARY_CXX_FLAGS)
@@ -168,13 +168,10 @@ macro (seqan_register_apps)
# .so when building DEVELOP. In the latter case it also encloses the
# static libs with -Bdynamic which turns static off for system libs.
# Here we remove these (so statics works), but only for NON-DEVELOP
- # on non-linux.
-
- # this one must not be unset on FreeBSD if not building APPs individually
- if ((CMAKE_SYSTEM_NAME MATCHES "Linux") OR (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP"))
- # make sure -rdynamic isn't added automatically
+ if (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP")
+ # make sure -Wl,-Bdynamic isn't added automatically
set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
- endif ((CMAKE_SYSTEM_NAME MATCHES "Linux") OR (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP"))
+ endif (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP")
endif (APPLE)
endif (SEQAN_STATIC_APPS AND (NOT CMAKE_SYSTEM_NAME MATCHES "Windows"))
From 3728cdba59905230d124e277a5c4efeea7c0cbcd Mon Sep 17 00:00:00 2001
From: Hannes Hauswedell
Date: Wed, 10 Feb 2016 16:42:47 +0100
Subject: [PATCH 06/26] [NOP] remove dead code
---
util/cmake/SeqAnBuildSystem.cmake | 27 ---------------------------
1 file changed, 27 deletions(-)
diff --git a/util/cmake/SeqAnBuildSystem.cmake b/util/cmake/SeqAnBuildSystem.cmake
index 1bbd86c698..c109f6d61a 100644
--- a/util/cmake/SeqAnBuildSystem.cmake
+++ b/util/cmake/SeqAnBuildSystem.cmake
@@ -47,22 +47,6 @@
include (SeqAnUsabilityAnalyzer)
include (CheckCXXCompilerFlag)
-# ---------------------------------------------------------------------------
-# Normalize CMAKE_CXX_FLAGS to be a string.
-#
-# If we do not do this then setting the environment variable CXXFLAGS will
-# cause CMAKE_CXX_FLAGS to become a list and this will generate compiler
-# command lines including the list item separator semicolon ";". This makes
-# the compiler command fail.
-# ---------------------------------------------------------------------------
-
-#if (CMAKE_CXX_FLAGS)
-# foreach (_FLAG ${CMAKE_CXX_FLAGS})
-# set (_FLAGS "${_FLAGS} ${_FLAG}")
-# endforeach (_FLAG ${CMAKE_CXX_FLAGS})
-# set (CMAKE_CXX_FLAGS "${_FLAGS}")
-#endif (CMAKE_CXX_FLAGS)
-
# ---------------------------------------------------------------------------
# Enable /bigobj flag on Windows.
# ---------------------------------------------------------------------------
@@ -122,17 +106,6 @@ function (add_executable NAME)
seqan_add_sua_dependency (${NAME})
endfunction (add_executable)
-# ---------------------------------------------------------------------------
-# Macro seqan_add_app_subdirectory (APP_NAME)
-# ---------------------------------------------------------------------------
-
-# macro (seqan_add_app_subdirectory APP_NAME)
-# if (("${SEQAN_BUILD_SYSTEM}" STREQUAL "SEQAN_RELEASE") OR
-# "${SEQAN_BUILD_SYSTEM}" STREQUAL "APP:${APP_NAME}")
-# add_subdirectory (${APP_NAME})
-# endif ()
-# endmacro (seqan_add_app_subdirectory)
-
# ---------------------------------------------------------------------------
# Macro seqan_register_apps ()
#
From 38fa337777b9c8311f2397a6c3f7ec47c45c8799 Mon Sep 17 00:00:00 2001
From: marehr
Date: Thu, 11 Feb 2016 20:01:28 +0100
Subject: [PATCH 07/26] [INTERNAL] #525: remove SEQAN_CHECKPOINT lines
Removed SEQAN_CHECKPOINT lines with
```find . -path ./.git -prune -o -type f -name "*" -print0 | xargs -0 perl -p -i -e 's/.*?SEQAN_CHECKPOINT.*?\n//g'```
---
apps/bs_tools/bisar_score.h | 2 -
apps/bs_tools/bisar_score_data.h | 10 ---
apps/bs_tools/casbar_score_data.h | 6 --
apps/fiona/index_qgram_parallel.h | 5 --
apps/gustaf/msplazer_out.h | 1 -
apps/razers/razers.h | 3 -
apps/splazers/razers.h | 3 -
apps/splazers/razers_spliced.h | 2 -
include/seqan/align/align_config.h | 16 ----
include/seqan/align/align_iterator_base.h | 45 ----------
include/seqan/align/dp_traceback_adaptor.h | 2 +-
include/seqan/align/fragment.h | 10 ---
include/seqan/align/gaps_anchor.h | 8 --
include/seqan/align/gaps_iterator_anchor.h | 6 --
include/seqan/basic/allocator_chunkpool.h | 9 --
include/seqan/basic/allocator_multipool.h | 8 --
include/seqan/basic/allocator_simple.h | 7 --
include/seqan/basic/alphabet_math.h | 4 -
include/seqan/basic/alphabet_residue.h | 1 -
include/seqan/basic/basic_tangle.h | 1 -
include/seqan/basic/basic_type.h | 3 -
include/seqan/basic/fundamental_transport.h | 12 ---
include/seqan/basic/holder_simple.h | 22 -----
include/seqan/basic/holder_tristate.h | 58 -------------
include/seqan/basic/hosted_type_interface.h | 10 ---
include/seqan/basic/iterator_adapt_std.h | 14 ---
include/seqan/basic/iterator_adaptor.h | 44 ----------
include/seqan/basic/iterator_base.h | 12 ---
include/seqan/basic/iterator_interface.h | 23 -----
include/seqan/basic/math_functions.h | 1 -
include/seqan/basic/proxy_base.h | 24 -----
include/seqan/basic/proxy_iterator.h | 5 --
include/seqan/consensus/consensus_base.h | 2 -
include/seqan/consensus/consensus_library.h | 3 -
include/seqan/file/string_mmap.h | 6 --
include/seqan/find/find_abndm.h | 11 ---
include/seqan/find/find_ahocorasick.h | 2 -
include/seqan/find/find_base.h | 38 --------
include/seqan/find/find_bndm.h | 5 --
include/seqan/find/find_bom.h | 3 -
include/seqan/find/find_hamming_simple.h | 5 --
include/seqan/find/find_horspool.h | 5 --
include/seqan/find/find_multi.h | 10 ---
include/seqan/find/find_multiple_bfam.h | 2 -
include/seqan/find/find_multiple_shiftand.h | 7 --
include/seqan/find/find_myers_ukkonen.h | 16 ----
include/seqan/find/find_pattern_base.h | 4 -
include/seqan/find/find_pex.h | 8 --
include/seqan/find/find_set_horspool.h | 3 -
include/seqan/find/find_shiftand.h | 5 --
include/seqan/find/find_shiftor.h | 6 --
include/seqan/find/find_wild_shiftand.h | 49 -----------
include/seqan/find/find_wumanber.h | 3 -
.../graph_algorithm_heap_tree.h | 26 ------
.../graph_algorithms/graph_algorithm_hmm.h | 12 ---
.../graph_algorithm_lis_his.h | 6 --
.../graph_algorithm_refine_align.h | 4 -
.../graph_algorithm_refine_aligngraph.h | 3 -
.../graph_algorithm_refine_annotation.h | 13 ---
.../graph_algorithm_refine_exact.h | 11 ---
.../graph_algorithm_refine_exact_iterative.h | 10 ---
.../graph_algorithm_refine_fragment.h | 6 --
.../graph_algorithm_refine_inexact.h | 7 --
include/seqan/graph_align/graph_impl_align.h | 48 ----------
.../graph_align/graph_impl_align_adapt.h | 17 ----
.../graph_msa/graph_align_tcoffee_base.h | 7 --
.../graph_msa/graph_align_tcoffee_distance.h | 3 -
.../graph_msa/graph_align_tcoffee_guidetree.h | 7 --
.../seqan/graph_msa/graph_align_tcoffee_io.h | 10 ---
.../graph_msa/graph_align_tcoffee_kmer.h | 2 -
.../graph_msa/graph_align_tcoffee_library.h | 13 ---
.../graph_align_tcoffee_progressive.h | 3 -
include/seqan/graph_types/graph_drawing.h | 13 ---
include/seqan/graph_types/graph_edgestump.h | 41 ---------
include/seqan/graph_types/graph_idmanager.h | 22 -----
.../seqan/graph_types/graph_impl_automaton.h | 42 ---------
include/seqan/graph_types/graph_impl_hmm.h | 42 ---------
include/seqan/graph_types/graph_impl_oracle.h | 2 -
include/seqan/graph_types/graph_impl_tree.h | 44 ----------
include/seqan/graph_types/graph_impl_trie.h | 2 -
.../seqan/graph_types/graph_impl_undirected.h | 30 -------
.../seqan/graph_types/graph_impl_wordgraph.h | 9 --
include/seqan/graph_types/graph_interface.h | 1 -
.../graph_types/graph_iterator_adjacency.h | 21 -----
.../seqan/graph_types/graph_iterator_bfs.h | 18 ----
.../seqan/graph_types/graph_iterator_dfs.h | 18 ----
.../seqan/graph_types/graph_iterator_edge.h | 22 -----
.../graph_types/graph_iterator_outedge.h | 87 -------------------
.../seqan/graph_types/graph_iterator_vertex.h | 21 -----
include/seqan/index/find_index.h | 18 ----
include/seqan/index/find_pigeonhole.h | 4 -
include/seqan/index/find_quasar.h | 2 -
include/seqan/index/find_swift.h | 4 -
include/seqan/index/index_dfi.h | 3 -
include/seqan/index/index_esa_drawing.h | 1 -
include/seqan/index/index_pizzachili.h | 20 -----
include/seqan/index/index_pizzachili_find.h | 4 -
include/seqan/index/index_pizzachili_string.h | 56 ------------
include/seqan/index/index_qgram.h | 16 ----
include/seqan/index/index_sa_mm.h | 1 -
include/seqan/index/index_sa_qsort.h | 3 -
include/seqan/index/index_shims.h | 53 -----------
include/seqan/index/index_skew3.h | 1 -
include/seqan/index/index_skew7.h | 1 -
include/seqan/index/shape_base.h | 11 ---
include/seqan/index/shape_gapped.h | 7 --
include/seqan/index/shape_onegapped.h | 6 --
include/seqan/index/shape_threshold.h | 1 -
.../journaled_set_journal_trace_descriptor.h | 6 --
include/seqan/map/map_adapter_stl.h | 47 ----------
include/seqan/misc/dequeue.h | 2 -
include/seqan/misc/interval_tree.h | 16 ----
include/seqan/misc/priority_type_heap.h | 14 ---
include/seqan/misc/svg.h | 1 -
include/seqan/modifier/modifier_alphabet.h | 54 ------------
.../modifier/modifier_alphabet_expansion.h | 16 ----
include/seqan/pipe/pipe_base.h | 17 ----
include/seqan/pipe/pool_base.h | 4 -
include/seqan/random/random_util.h | 1 -
include/seqan/score/score_base.h | 7 --
include/seqan/score/score_edit.h | 8 --
include/seqan/score/score_matrix.h | 8 --
include/seqan/score/score_matrix_data.h | 9 --
include/seqan/score/score_simple.h | 14 ---
include/seqan/seeds/basic_iter_indirect.h | 11 ---
include/seqan/seeds/seeds_extension.h | 1 -
include/seqan/seeds/seeds_seed_chained.h | 2 -
.../seqan/seeds/seeds_seed_set_unordered.h | 1 -
include/seqan/sequence/adapt_array_pointer.h | 57 ------------
include/seqan/sequence/segment_base.h | 18 ----
include/seqan/sequence/segment_infix.h | 55 ------------
include/seqan/sequence/segment_prefix.h | 37 --------
include/seqan/sequence/segment_suffix.h | 51 -----------
.../seqan/sequence/sequence_concatenator.h | 2 -
include/seqan/sequence/sequence_interface.h | 66 --------------
include/seqan/sequence/sequence_lexical.h | 34 --------
include/seqan/sequence/string_block.h | 28 ------
include/seqan/sequence/string_cstyle.h | 57 ------------
include/seqan/sequence/string_packed.h | 1 -
include/seqan/sequence/string_packed_old.h | 71 ---------------
include/seqan/sequence/string_set_base.h | 7 --
.../seqan/sequence/string_set_concat_direct.h | 2 -
.../sequence/string_set_dependent_generous.h | 10 ---
.../sequence/string_set_dependent_tight.h | 10 ---
include/seqan/sequence/string_set_owner.h | 7 --
include/seqan/sequence/string_set_segment.h | 2 -
.../journal_entries_sorted_array.h | 5 --
.../sequence_journaled/sequence_journaled.h | 36 --------
.../sequence_journaled_iterator.h | 37 --------
.../sequence_journaled_iterator_fast.h | 1 -
include/seqan/statistics/statistics_base.h | 1 -
include/seqan/store/store_all.h | 2 -
tests/basic/test_basic_iterator.h | 3 -
tests/find/test_find.cpp | 3 -
tests/sequence/test_segment.h | 3 -
tests/sequence/test_string.h | 12 ---
tests/sequence/test_stringset.h | 7 --
157 files changed, 1 insertion(+), 2288 deletions(-)
diff --git a/apps/bs_tools/bisar_score.h b/apps/bs_tools/bisar_score.h
index d40048a677..73e44bdb16 100644
--- a/apps/bs_tools/bisar_score.h
+++ b/apps/bs_tools/bisar_score.h
@@ -521,14 +521,12 @@ scoreGapExtendHorizontal(
template
inline int
scoreGapExtend(Score > const & /*me*/) {
- SEQAN_CHECKPOINT;
//std::cout << "This should happen only once: scoreGapExtend()"<< std::endl;
return (int)-100;
}
template
inline int
scoreGapOpen(Score > const & /*me*/) {
- SEQAN_CHECKPOINT;
//std::cout << "This should happen only once: scoreGapOpen()" << std::endl;
return (int)-200;
}
diff --git a/apps/bs_tools/bisar_score_data.h b/apps/bs_tools/bisar_score_data.h
index 1978e40956..69fb77203c 100644
--- a/apps/bs_tools/bisar_score_data.h
+++ b/apps/bs_tools/bisar_score_data.h
@@ -142,7 +142,6 @@ struct SeqErrorFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
// Column sum must be 1 (in the current model)
static TValue const _data[TAB_SIZE] = {
@@ -167,7 +166,6 @@ struct SeqErrorFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue fE = 1.0/3.0; // Column sum must be 1
static TValue const _data[TAB_SIZE] = {
@@ -192,7 +190,6 @@ struct SeqErrorFreqsTo {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 1.0/5.0;
// A, C, G, T, N
static TValue const _data[VALUE_SIZE] = {f, f, f, f, f}; // siehe Dohm et.al. 2011
@@ -209,7 +206,6 @@ struct SeqErrorFreqsTo {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
// A, C, G, T, N
static TValue const _data[VALUE_SIZE] = {0.25, 0.38, 0.16, 0.21, 0.2}; // siehe Dohm et.al. 2011 // TODO N?
@@ -227,7 +223,6 @@ struct BaseErrorFreqsFrom {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
// A, C, G, T N
static TValue const _data[VALUE_SIZE] = {0.25, 0.19, 0.24, 0.33, 0.0}; // siehe Dohm et.al. 2008
return _data; // N stays N
@@ -241,7 +236,6 @@ struct BaseErrorFreqsFrom {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 1.0/5.0;
// A, C, G, T N
static TValue const _data[VALUE_SIZE] = {f, f, f, f, f}; // siehe Dohm et.al. 2008
@@ -262,7 +256,6 @@ struct InsErrorFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
// A, C, G, T, N
static TValue const _data[VALUE_SIZE] = {0.43, 0.065, 0.065, 0.43, 0.01}; // siehe Dohm et.al. 2011 // TODO N?
@@ -277,7 +270,6 @@ struct InsErrorFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 1.0/5.0;
static TValue const _data[VALUE_SIZE] = {f, f, f, f, f};
return _data;
@@ -295,7 +287,6 @@ struct DelErrorFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
// A, C, G, T, N
static TValue const _data[VALUE_SIZE] = {0.42, 0.075, 0.075, 0.42, 0.00}; // siehe Dohm et.al. 2011
@@ -310,7 +301,6 @@ struct DelErrorFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 1.0/5.0;
static TValue const _data[VALUE_SIZE] = {f, f, f, f, f};
return _data;
diff --git a/apps/bs_tools/casbar_score_data.h b/apps/bs_tools/casbar_score_data.h
index 7d7880f8e5..02ca6809e1 100644
--- a/apps/bs_tools/casbar_score_data.h
+++ b/apps/bs_tools/casbar_score_data.h
@@ -20,7 +20,6 @@ struct SeqErrorFreqsN { // TODO -> BsNonSimple
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
// Column sum must be 1 (in the current model)
static TValue const _data[TAB_SIZE] = {
@@ -45,7 +44,6 @@ struct SeqErrorFreqsN {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue fE = 1.0/3.0; // Column sum must be 1
static TValue const _data[TAB_SIZE] = {
@@ -73,7 +71,6 @@ struct ReadBaseFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 0.9/4.0;
static TValue const _data[TAB_SIZE] = {f, f, f, f, 0.4/4.0}; // TODO bs case
@@ -89,7 +86,6 @@ struct ReadBaseFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 0.9/4.0;
static TValue const _data[TAB_SIZE] = {f, f, f, f, 0.4/4.0}; // TODO bs case
@@ -109,7 +105,6 @@ struct RefBaseFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 0.9/4.0;
static TValue const _data[TAB_SIZE] = {f, f, f, f, 0.4/4.0};
@@ -125,7 +120,6 @@ struct RefBaseFreqs {
};
static inline TValue const * getData() {
- SEQAN_CHECKPOINT;
TValue f = 0.9/4.0;
static TValue const _data[TAB_SIZE] = {f, f, f, f, 0.4/4.0};
diff --git a/apps/fiona/index_qgram_parallel.h b/apps/fiona/index_qgram_parallel.h
index 69b36418d8..cb6c4106bd 100644
--- a/apps/fiona/index_qgram_parallel.h
+++ b/apps/fiona/index_qgram_parallel.h
@@ -118,7 +118,6 @@ template < typename TDir, typename TBucketMap, typename TText, typename TShape,
inline void
_qgramCountQGrams(TDir &dir, TBucketMap &bucketMap, TText const &text, TShape shape, TStepSize stepSize, Tag parallelTag)
{
-SEQAN_CHECKPOINT
typedef typename Iterator::Type TIterator;
typedef typename Iterator::Type TDirIterator;
typedef typename Value::Type TSize;
@@ -161,7 +160,6 @@ template < typename TDir, typename TBucketMap, typename TString, typename TSpec,
inline void
_qgramCountQGrams(TDir &dir, TBucketMap &bucketMap, StringSet const &stringSet, TShape shape, TStepSize stepSize, Tag parallelTag)
{
-SEQAN_CHECKPOINT
typedef typename Iterator::Type TIterator;
typedef typename Iterator::Type TDirIterator;
typedef typename Value::Type TSize;
@@ -327,7 +325,6 @@ _qgramFillSuffixArray(
TWithConstraints const,
Tag parallelTag)
{
-SEQAN_CHECKPOINT
typedef typename Iterator::Type TIterator;
typedef typename Iterator::Type TDirIterator;
typedef typename Value::Type TSize;
@@ -403,7 +400,6 @@ _qgramFillSuffixArray(
TWithConstraints const,
Tag parallelTag)
{
-SEQAN_CHECKPOINT
typedef typename Iterator::Type TIterator;
typedef typename Iterator::Type TDirIterator;
typedef typename Value::Type TSize;
@@ -482,7 +478,6 @@ template < typename TDir, typename TParallelTag >
inline void
_qgramPostprocessBuckets(TDir &dir, Tag parallelTag)
{
-SEQAN_CHECKPOINT
typedef typename Iterator::Type TDirIterator;
typedef typename Size::Type TSize;
typedef typename Value::Type TValue;
diff --git a/apps/gustaf/msplazer_out.h b/apps/gustaf/msplazer_out.h
index 7acaafb2d4..c3b558e1ef 100644
--- a/apps/gustaf/msplazer_out.h
+++ b/apps/gustaf/msplazer_out.h
@@ -68,7 +68,6 @@ write(std::ostream & out,
DotDrawingMSplazer const &)
{
// IOREV _doc_ _batchreading_
- SEQAN_CHECKPOINT
// typedef typename Value::Type TBreakpoint; // Requires Value specialisation in msplazer.h
typedef typename TBreakpoint::TId TId;
diff --git a/apps/razers/razers.h b/apps/razers/razers.h
index 39186dd6ed..3c45196044 100644
--- a/apps/razers/razers.h
+++ b/apps/razers/razers.h
@@ -1804,7 +1804,6 @@ void mapSingleReads(
TValue prefixLen,
MicroRNA)
{
- SEQAN_CHECKPOINT
typedef typename Value::Type TString;
typedef typename Iterator::Type TIterator;
typedef typename Value::Type TSize;
@@ -1844,7 +1843,6 @@ void mapSingleReads(
inline void
_qgramCountQGrams(TDir &dir, TStringSet &stringSet, TShape &shape, TValue prefixLen, MicroRNA)
{
- SEQAN_CHECKPOINT
typedef typename Value::Type TString;
typedef typename Iterator::Type TIterator;
typedef typename Value::Type TSize;
@@ -1869,7 +1867,6 @@ void mapSingleReads(
template < typename TIndex, typename TValue>
void createQGramIndex(TIndex &index, TValue prefixLen, MicroRNA)
{
- SEQAN_CHECKPOINT
typename Fibre::Type &text = indexText(index);
typename Fibre::Type &sa = indexSA(index);
typename Fibre::Type &dir = indexDir(index);
diff --git a/apps/splazers/razers.h b/apps/splazers/razers.h
index ae5d89d729..853a5a8b16 100644
--- a/apps/splazers/razers.h
+++ b/apps/splazers/razers.h
@@ -1745,7 +1745,6 @@ void mapSingleReads(
TValue prefixLen,
MicroRNA)
{
- SEQAN_CHECKPOINT
typedef typename Value::Type TString;
typedef typename Iterator::Type TIterator;
typedef typename Value::Type TSize;
@@ -1785,7 +1784,6 @@ void mapSingleReads(
inline void
_qgramCountQGrams(TDir &dir, TStringSet &stringSet, TShape &shape, TValue prefixLen, MicroRNA)
{
- SEQAN_CHECKPOINT
typedef typename Value::Type TString;
typedef typename Iterator::Type TIterator;
typedef typename Value::Type TSize;
@@ -1810,7 +1808,6 @@ void mapSingleReads(
template < typename TIndex, typename TValue>
void createQGramIndex(TIndex &index, TValue prefixLen, MicroRNA)
{
- SEQAN_CHECKPOINT
typename Fibre::Type &text = indexText(index);
typename Fibre::Type &sa = indexSA(index);
typename Fibre::Type &dir = indexDir(index);
diff --git a/apps/splazers/razers_spliced.h b/apps/splazers/razers_spliced.h
index 798e2489d3..d62852e2ff 100644
--- a/apps/splazers/razers_spliced.h
+++ b/apps/splazers/razers_spliced.h
@@ -1169,7 +1169,6 @@ _alignBandedNeedlemanWunschTrace(TAlign& align,
TDiagonal const diagL,
TDiagonal const diagU)
{
- SEQAN_CHECKPOINT
typedef typename Value::Type TString;
typedef typename Id::Type TId;
typedef typename Size::Type TSize;
@@ -1290,7 +1289,6 @@ _alignBandedNeedlemanWunsch(TTrace& trace,
String::Type,int> > & maxCols,
unsigned minColNum)
{
- SEQAN_CHECKPOINT
typedef typename Value::Type TTraceValue;
typedef typename Value::Type TScoreValue;
typedef typename Value::Type TString;
diff --git a/include/seqan/align/align_config.h b/include/seqan/align/align_config.h
index c90c0662b6..480dad9144 100644
--- a/include/seqan/align/align_config.h
+++ b/include/seqan/align/align_config.h
@@ -109,7 +109,6 @@ _initFirstColumn(AlignConfig const,
TElement& element,
TCost const cost)
{
- SEQAN_CHECKPOINT
element = cost;
}
@@ -121,7 +120,6 @@ _initFirstColumn(AlignConfig const,
TElement& element,
TCost const)
{
- SEQAN_CHECKPOINT
element = 0;
}
@@ -133,7 +131,6 @@ _initFirstRow(AlignConfig const,
TElement& element,
TCost const cost)
{
- SEQAN_CHECKPOINT
element = cost;
}
@@ -145,7 +142,6 @@ _initFirstRow(AlignConfig const,
TElement& element,
TCost const)
{
- SEQAN_CHECKPOINT
element = 0;
}
@@ -162,7 +158,6 @@ _lastRow(AlignConfig const,
TValue2 const,
TIndex2 const)
{
- SEQAN_CHECKPOINT
// Nop
}
@@ -176,7 +171,6 @@ _lastRow(AlignConfig const,
TValue2 const val,
TIndex2 const index)
{
- SEQAN_CHECKPOINT
if (val > maxValue[0]) {
maxValue[0] = val;
maxIndex[0] = index;
@@ -192,7 +186,6 @@ _lastColumn(AlignConfig const,
TIndex1&,
TColumn const& column)
{
- SEQAN_CHECKPOINT
maxValue[1] = column[length(column) - 1];
}
@@ -205,7 +198,6 @@ _lastColumn(AlignConfig const,
TIndex1& maxIndex,
TColumn const& column)
{
- SEQAN_CHECKPOINT;
typedef typename Size::Type TSize;
typedef typename Iterator::Type TColIter;
TSize limit = length(column) - 1;
@@ -230,7 +222,6 @@ _maxOfAlignment(AlignConfig const,
TSize const,
TSize const)
{
- SEQAN_CHECKPOINT
return maxValue[1];
}
@@ -244,7 +235,6 @@ _maxOfAlignment(AlignConfig const,
TSize const len1,
TSize const)
{
- SEQAN_CHECKPOINT
maxIndex[0] = len1;
return maxValue[1];
}
@@ -259,7 +249,6 @@ _maxOfAlignment(AlignConfig const,
TSize const,
TSize const len2)
{
- SEQAN_CHECKPOINT
maxIndex[1] = len2;
return maxValue[0];
}
@@ -274,7 +263,6 @@ _maxOfAlignment(AlignConfig const,
TSize const len1,
TSize const len2)
{
- SEQAN_CHECKPOINT
// Find the maximum
if (maxValue[1] > maxValue[0]) maxIndex[0] = len1;
else maxIndex[1] = len2;
@@ -292,7 +280,6 @@ _lastColumn(AlignConfig const,
TIndex2 const row,
TIndex2 const col)
{
- SEQAN_CHECKPOINT
maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col;
}
@@ -307,7 +294,6 @@ _lastColumn(AlignConfig const,
TIndex2 const row,
TIndex2 const col)
{
- SEQAN_CHECKPOINT
if (val > maxValue[1]) {maxValue[1] = val; maxIndex[2] = row; maxIndex[3] = col; }
}
@@ -322,7 +308,6 @@ _lastRow(AlignConfig const,
TIndex2 const row,
TIndex2 const col)
{
- SEQAN_CHECKPOINT
maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col;
}
@@ -337,7 +322,6 @@ _lastRow(AlignConfig const,
TIndex2 const row,
TIndex2 const col)
{
- SEQAN_CHECKPOINT
if (val > maxValue[0]) {maxValue[0] = val; maxIndex[0] = row; maxIndex[1] = col; }
}
diff --git a/include/seqan/align/align_iterator_base.h b/include/seqan/align/align_iterator_base.h
index 8a4f455dca..89b9e1f807 100644
--- a/include/seqan/align/align_iterator_base.h
+++ b/include/seqan/align/align_iterator_base.h
@@ -72,19 +72,16 @@ class Iter >
public:
Iter()
{
-SEQAN_CHECKPOINT
}
Iter(TAlign & _align):
data_host(& _align)
{
-SEQAN_CHECKPOINT
typename Position::Type _i = length(rows(_align));
resize(data_iterators, _i, Exact());
}
Iter(TAlign & _align, TRowPosition _pos):
data_host(& _align)
{
-SEQAN_CHECKPOINT
typename Position::Type _i = length(rows(_align));
resize(data_iterators, _i, Exact());
@@ -101,13 +98,11 @@ SEQAN_CHECKPOINT
}
~Iter()
{
-SEQAN_CHECKPOINT
}
Iter const &
operator = (Iter const & _other)
{
-SEQAN_CHECKPOINT
data_host = _other.data_host;
data_iterators = _other.data_iterators;
return *this;
@@ -123,14 +118,12 @@ template
inline TAlign &
host(Iter > & me)
{
-SEQAN_CHECKPOINT
return *me.data_host;
}
template
inline TAlign &
host(Iter > const & me)
{
-SEQAN_CHECKPOINT
return *me.data_host;
}
@@ -140,7 +133,6 @@ template
inline void
setHost(Iter > & me, TAlign & _host)
{
-SEQAN_CHECKPOINT
me.data_host = & _host;
}
@@ -150,14 +142,12 @@ template
inline typename Cols::Type
container(Iter > & me)
{
-SEQAN_CHECKPOINT
return cols(*me.data_host);
}
template
inline typename Cols::Type
container(Iter > const & me)
{
-SEQAN_CHECKPOINT
return cols(*me.data_host);
}
@@ -167,7 +157,6 @@ template
inline void
goNext(Iter > & me)
{
-SEQAN_CHECKPOINT
typedef typename Row::Type TRow;
typedef typename Iterator::Type TRowIterator;
typedef String TIterators;
@@ -188,7 +177,6 @@ template
inline Iter > &
operator ++(Iter > & me)
{
-SEQAN_CHECKPOINT
goNext(me);
return me;
}
@@ -198,7 +186,6 @@ template
inline Iter >
operator ++(Iter > & me, int)
{
-SEQAN_CHECKPOINT
Iter > ret = me;
goNext(me);
return ret;
@@ -210,7 +197,6 @@ template
inline void
goPrevious(Iter > & me)
{
-SEQAN_CHECKPOINT
typedef typename Row::Type TRow;
typedef typename Iterator::Type TRowIterator;
typedef String TIterators;
@@ -231,7 +217,6 @@ template
inline Iter > &
operator --(Iter > & me)
{
-SEQAN_CHECKPOINT
goPrevious(me);
return me;
}
@@ -241,7 +226,6 @@ template
inline Iter >
operator --(Iter > & me, int)
{
-SEQAN_CHECKPOINT
Iter > ret = me;
goPrevious(me);
return ret;
@@ -254,7 +238,6 @@ inline bool
operator ==(Iter > & _left,
Iter > & _right)
{
-SEQAN_CHECKPOINT
return getValue(_left.data_iterators, 0) == getValue(_right.data_iterators, 0);
}
template
@@ -262,7 +245,6 @@ inline bool
operator ==(Iter > const & _left,
Iter > & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
}
template
@@ -270,7 +252,6 @@ inline bool
operator ==(Iter > & _left,
Iter > const & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
}
template
@@ -278,7 +259,6 @@ inline bool
operator ==(Iter > const & _left,
Iter > const & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) == value(_right.data_iterators, 0);
}
@@ -289,7 +269,6 @@ inline bool
operator !=(Iter > & _left,
Iter > & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
}
template
@@ -297,7 +276,6 @@ inline bool
operator !=(Iter > const & _left,
Iter > & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
}
template
@@ -305,7 +283,6 @@ inline bool
operator !=(Iter > & _left,
Iter > const & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
}
template
@@ -313,7 +290,6 @@ inline bool
operator !=(Iter > const & _left,
Iter > const & _right)
{
-SEQAN_CHECKPOINT
return value(_left.data_iterators, 0) != value(_right.data_iterators, 0);
}
@@ -324,7 +300,6 @@ inline typename Reference::Type
value(Iter > & me,
TPosition pos_)
{
-SEQAN_CHECKPOINT
return value(me.data_iterators[pos_]);
}
template
@@ -332,7 +307,6 @@ inline typename Reference::Type
value(Iter > const & me,
TPosition pos_)
{
-SEQAN_CHECKPOINT
return value(me.data_iterators[pos_]);
}
//////////////////////////////////////////////////////////////////////////////
@@ -342,7 +316,6 @@ inline typename GetValue::Type
getValue(Iter > & me,
TPosition pos_)
{
-SEQAN_CHECKPOINT
return getValue(me.data_iterators[pos_]);
}
template
@@ -350,7 +323,6 @@ inline typename GetValue::Type
getValue(Iter > const & me,
TPosition pos_)
{
-SEQAN_CHECKPOINT
return getValue(me.data_iterators[pos_]);
}
@@ -362,7 +334,6 @@ assignValue(Iter > & me,
TPosition pos_,
TValue & val)
{
-SEQAN_CHECKPOINT
return assignValue(me.data_iterators[pos_], val);
}
template
@@ -371,7 +342,6 @@ assignValue(Iter > & me,
TPosition pos_,
TValue const & val)
{
-SEQAN_CHECKPOINT
return assignValue(me.data_iterators[pos_], val);
}
template
@@ -380,7 +350,6 @@ assignValue(Iter > const & me,
TPosition pos_,
TValue & val)
{
-SEQAN_CHECKPOINT
return assignValue(me.data_iterators[pos_], val);
}
template
@@ -389,7 +358,6 @@ assignValue(Iter > const & me,
TPosition pos_,
TValue const & val)
{
-SEQAN_CHECKPOINT
return assignValue(me.data_iterators[pos_], val);
}
@@ -401,7 +369,6 @@ moveValue(Iter > & me,
TPosition pos_,
TValue & val)
{
-SEQAN_CHECKPOINT
return moveValue(me.data_iterators[pos_], val);
}
template
@@ -410,7 +377,6 @@ moveValue(Iter > & me,
TPosition pos_,
TValue const & val)
{
-SEQAN_CHECKPOINT
return moveValue(me.data_iterators[pos_], val);
}
template
@@ -419,7 +385,6 @@ moveValue(Iter > const & me,
TPosition pos_,
TValue & val)
{
-SEQAN_CHECKPOINT
return moveValue(me.data_iterators[pos_], val);
}
template
@@ -428,7 +393,6 @@ moveValue(Iter > const & me,
TPosition pos_,
TValue const & val)
{
-SEQAN_CHECKPOINT
return moveValue(me.data_iterators[pos_], val);
}
@@ -442,7 +406,6 @@ inline Iter > &
operator +=(Iter > & me,
TSize size)
{
-SEQAN_CHECKPOINT
typedef typename Row::Type TRow;
typedef typename Iterator::Type TRowIterator;
typedef String TIterators;
@@ -467,7 +430,6 @@ inline Iter >
operator +(Iter > & me,
TSize size)
{
-SEQAN_CHECKPOINT
Iter > ret = me;
me += size;
return me;
@@ -477,7 +439,6 @@ inline Iter >
operator +(Iter > const & me,
TSize size)
{
-SEQAN_CHECKPOINT
Iter > ret = me;
me += size;
return me;
@@ -490,7 +451,6 @@ inline Iter > &
operator -=(Iter > & me,
TSize size)
{
-SEQAN_CHECKPOINT
typedef typename Row::Type TRow;
typedef typename Iterator::Type TRowIterator;
typedef String TIterators;
@@ -514,7 +474,6 @@ inline Iter >
operator -(Iter > & me,
TSize size)
{
-SEQAN_CHECKPOINT
Iter > ret = me;
me -= size;
return me;
@@ -524,7 +483,6 @@ inline Iter >
operator -(Iter > const & me,
TSize size)
{
-SEQAN_CHECKPOINT
Iter > ret = me;
me -= size;
return me;
@@ -537,7 +495,6 @@ inline typename Difference::Type
operator -(Iter > const & left,
Iter > const & right)
{
-SEQAN_CHECKPOINT
SEQAN_ASSERT_GT(length(left.data_iterators), 0u);
SEQAN_ASSERT_GT(length(right.data_iterators), 0u);
@@ -550,14 +507,12 @@ template
inline typename Position::Type
position(Iter > & me)
{
-SEQAN_CHECKPOINT
return position(me.data_iterators[0], row(host(me), 0));
}
template
inline typename Position::Type
position(Iter > const & me)
{
-SEQAN_CHECKPOINT
return position(me.data_iterators[0], row(host(me), 0));
}
*/
diff --git a/include/seqan/align/dp_traceback_adaptor.h b/include/seqan/align/dp_traceback_adaptor.h
index 040daac67e..3b0d43f43f 100644
--- a/include/seqan/align/dp_traceback_adaptor.h
+++ b/include/seqan/align/dp_traceback_adaptor.h
@@ -277,7 +277,7 @@ _adaptTraceSegmentsTo(String, TStringSpec> & matc
// if (tv == Horizontal) {
// for (int i = pos1 + segLen - 1; i>= (int) pos1;--i) {
// resize(value(nodeString, index), len1 + len2, nilVertex);
-// TStringIter it = beSEQAN_CHECKPOINTgin(value(nodeString, index));
+// TStringIter it = begin(value(nodeString, index));
// for(TPos all = 0;all const& f,
TStringSet& str,
TVal const seqId)
{
- SEQAN_CHECKPOINT
typedef typename Id >::Type TId;
return ((TId) seqId == (f.seqId1)) ? infix(getValueById(str, (TId) seqId), f.begin1, f.begin1 + f.len) : infix(getValueById(str, (TId) seqId), f.begin2, f.begin2 + f.len);
}
@@ -344,7 +343,6 @@ inline typename Id >::Type &
sequenceId(Fragment & f,
TVal const seqId)
{
- SEQAN_CHECKPOINT
return (seqId == (TVal)0) ? f.seqId1 : f.seqId2;
}
@@ -353,7 +351,6 @@ inline typename Id >::Type const &
sequenceId(Fragment const & f,
TVal const seqId)
{
- SEQAN_CHECKPOINT
return (seqId == (TVal)0) ? f.seqId1 : f.seqId2;
}
@@ -376,7 +373,6 @@ inline TSize&
fragmentBegin(Fragment const& f,
TVal const seqId)
{
- SEQAN_CHECKPOINT
typedef typename Id >::Type TId;
return ((TId) seqId == f.seqId1) ? const_cast(f.begin1) : const_cast(f.begin2);
}
@@ -388,7 +384,6 @@ inline TSize&
fragmentLength(Fragment const& f,
TVal const)
{
- SEQAN_CHECKPOINT
return const_cast(f.len);
}
@@ -409,7 +404,6 @@ template
inline TSize&
fragmentLength(Fragment const& f)
{
- SEQAN_CHECKPOINT
return const_cast(f.len);
}
@@ -423,7 +417,6 @@ getProjectedPosition(Fragment > const& f,
TId2& seqId2,
TPosition2& pos2)
{
- SEQAN_CHECKPOINT
typedef typename Id >::Type TId;
if ((TId) seqId == f.seqId1) {
@@ -483,7 +476,6 @@ getProjectedPosition(Fragment > const& f,
TId2& seqId2,
TPosition2& pos2)
{
- SEQAN_CHECKPOINT
typedef typename Id >::Type TId;
if ((TId) seqId == f.seqId1) {
@@ -515,7 +507,6 @@ getProjectedPosition(Fragment > const& f,
TId2& seqId2,
TPosition2& pos2)
{
- SEQAN_CHECKPOINT
(void) seqId; // When compiled without assertions.
SEQAN_ASSERT((seg_num == 0 && seqId==f.seqId1) || (seg_num == 1 && seqId==f.seqId2));
@@ -553,7 +544,6 @@ template
inline bool
isReversed(Fragment > const& f)
{
- SEQAN_CHECKPOINT
return f.reversed;
}
diff --git a/include/seqan/align/gaps_anchor.h b/include/seqan/align/gaps_anchor.h
index b5a7acd8ff..0091f5b84c 100644
--- a/include/seqan/align/gaps_anchor.h
+++ b/include/seqan/align/gaps_anchor.h
@@ -518,7 +518,6 @@ template