diff --git a/recipes/softsv/softsv.patch b/recipes/softsv/softsv.patch index 6f763e386972e..8b44369d46ff4 100644 --- a/recipes/softsv/softsv.patch +++ b/recipes/softsv/softsv.patch @@ -1,7 +1,7 @@ -diff --git i/SoftSV_1.4.2/makefile w/SoftSV_1.4.2/makefile -index da3a2b0..dad1cef 100644 ---- i/SoftSV_1.4.2/makefile -+++ w/SoftSV_1.4.2/makefile +diff --git i/makefile w/makefile +index da3a2b0..0294964 100644 +--- i/makefile ++++ w/makefile @@ -2,7 +2,7 @@ # You may need to modify the following paths: @@ -25,13 +25,207 @@ index da3a2b0..dad1cef 100644 @echo 'Building target: $@' @echo 'Invoking: GCC C++ Linker' - $(CC) -o $@ $(OBJS) -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${BAMTOOLS}/lib -+ $(CC) -std=c++14 -o $@ $(OBJS) -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${PREFIX}/lib ++ $(CC) -std=c++14 -o $@ $(OBJS) -Wl,--copy-dt-needed-entries -lboost_program_options -lboost_system -lboost_filesystem -lbamtools -L${PREFIX}/lib @echo 'Finished building target: $@' @echo ' ' -diff --git i/SoftSV_1.4.2/src/Deletions.cpp w/src/Deletions.cpp +diff --git i/src/Analysis.d w/src/Analysis.d +index 8be3017..089db1c 100644 +--- i/src/Analysis.d ++++ w/src/Analysis.d +@@ -1220,6 +1220,8 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_gcc.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_nvcc.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_debug.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_test_system.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_helper.h \ +@@ -1308,9 +1310,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_tangle.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_view.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_device.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/simd.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base_seqan_impl.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/misc/bit_twiddling_functors.h \ +@@ -1344,6 +1343,8 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_owner.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_segment.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_critical_section.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_condition.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_tags.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_macros.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_atomic_primitives.h \ +@@ -1356,9 +1357,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_queue_suspendable.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_resource_pool.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_serializer.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local_iterator.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_thread_pool.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet_expansion.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_iterator.h \ +@@ -1372,7 +1370,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_shortcuts.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_cyclic_shape.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_position.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_padding.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_metafunctions.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_align.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score.h \ +@@ -1385,8 +1382,10 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_forwards.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_forwards.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_base.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_mutex.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_thread.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_sync.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event_win.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_async.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_directory.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/file/file_page.h \ +@@ -1409,7 +1408,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_io.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_data.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_dyn.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_simple.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/fragment.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_types.h \ +@@ -1479,7 +1477,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_config.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_traceback.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/matrix_base.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/aligned_sequence_concept.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_base.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_iterator_base.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_array.h \ +@@ -1492,11 +1489,11 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/alignment_algorithm_tags.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_profile.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_band.h \ ++ /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_linear.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_affine.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_dynamic.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_trace_segment.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_traceback_adaptor.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_formula.h \ +@@ -1519,7 +1516,6 @@ src/Analysis.d: src/Analysis.cpp src/Analysis.hpp src/GenomicRanges.hpp \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_myers_hirschberg_impl.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_waterman_eggert_impl.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h \ +- /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_interface_wrapper.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_unbanded.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_banded.h \ + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_unbanded.h \ +@@ -2753,6 +2749,8 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/platform.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_gcc.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/platform/platform_nvcc.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_debug.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_test_system.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/debug_helper.h: +@@ -2841,9 +2839,6 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_tangle.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_view.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/basic/basic_device.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/simd.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/simd/simd_base_seqan_impl.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/misc/bit_twiddling_functors.h: +@@ -2877,6 +2872,8 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_owner.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/sequence/string_set_segment.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_critical_section.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_condition.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_tags.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_macros.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_atomic_primitives.h: +@@ -2889,9 +2886,6 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_queue_suspendable.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_resource_pool.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_serializer.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/enumerable_thread_local_iterator.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/parallel/parallel_thread_pool.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_alphabet_expansion.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_iterator.h: +@@ -2905,7 +2899,6 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_shortcuts.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_cyclic_shape.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_position.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/modifier/modifier_padding.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_metafunctions.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_align.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score.h: +@@ -2918,8 +2911,10 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_forwards.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_forwards.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_base.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_mutex.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_thread.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_sync.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/system/system_event_win.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_async.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/system/file_directory.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/file/file_page.h: +@@ -2942,7 +2937,6 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_io.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_data.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_matrix_dyn.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/score/score_simple.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/fragment.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/graph_types.h: +@@ -3012,7 +3006,6 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_config.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_traceback.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/matrix_base.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/aligned_sequence_concept.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_base.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_iterator_base.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/gaps_array.h: +@@ -3025,11 +3018,11 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/alignment_algorithm_tags.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_profile.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_band.h: ++/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_linear.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_affine.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_cell_dynamic.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_scout.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_trace_segment.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_traceback_adaptor.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/dp_formula.h: +@@ -3052,7 +3045,6 @@ src/Misc.cpp: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_myers_hirschberg_impl.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_waterman_eggert_impl.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: +-/home/mgrigorov/miniconda3/envs/test123/include/seqan/align/align_interface_wrapper.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_unbanded.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/global_alignment_banded.h: + /home/mgrigorov/miniconda3/envs/test123/include/seqan/align/local_alignment_unbanded.h: +diff --git i/src/Deletions.cpp w/src/Deletions.cpp index 8ea7345..d44297d 100644 ---- i/SoftSV_1.4.2/src/Deletions.cpp +--- i/src/Deletions.cpp +++ w/src/Deletions.cpp @@ -20,6 +20,8 @@ * @date 2015/09/09 @@ -69,9 +263,9 @@ index 8ea7345..d44297d 100644 std::stringstream output, bpSeq; -diff --git i/SoftSV_1.4.2/src/Inversions.cpp w/src/Inversions.cpp +diff --git i/src/Inversions.cpp w/src/Inversions.cpp index 207a774..ff4f8d9 100644 ---- i/SoftSV_1.4.2/src/Inversions.cpp +--- i/src/Inversions.cpp +++ w/src/Inversions.cpp @@ -20,6 +20,8 @@ * @date 2015/09/09 @@ -109,9 +303,9 @@ index 207a774..ff4f8d9 100644 // Outpu format: // Chr Start End Support(PE) Support(SC) Upstream-breakpoint-sequence Downstream-breakpoint-sequence -diff --git i/SoftSV_1.4.2/src/Misc.cpp w/src/Misc.cpp +diff --git i/src/Misc.cpp w/src/Misc.cpp index bd10001..e0b460a 100644 ---- i/SoftSV_1.4.2/src/Misc.cpp +--- i/src/Misc.cpp +++ w/src/Misc.cpp @@ -32,6 +32,8 @@ @@ -122,9 +316,9 @@ index bd10001..e0b460a 100644 /** * @brief Returns the total length of small deletions within the CIGAR string of an alignment. -diff --git i/SoftSV_1.4.2/src/Tandems.cpp w/src/Tandems.cpp +diff --git i/src/Tandems.cpp w/src/Tandems.cpp index e6546af..7af0834 100644 ---- i/SoftSV_1.4.2/src/Tandems.cpp +--- i/src/Tandems.cpp +++ w/src/Tandems.cpp @@ -20,6 +20,8 @@ * @date 2015/09/09