[med-svn] [tophat] 04/05: Merge tag 'upstream/2.0.11+dfsg'
Andreas Tille
tille at debian.org
Wed Mar 19 10:56:45 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository tophat.
commit 34d992b9c437c9426eab751aacdeb5572e99e04a
Merge: 2569fee 8d67a5c
Author: Andreas Tille <tille at debian.org>
Date: Wed Mar 19 11:57:43 2014 +0100
Merge tag 'upstream/2.0.11+dfsg'
Upstream version 2.0.11+dfsg
src/SeqAn-1.3/COPYING | 674 ----
src/SeqAn-1.3/README | 22 -
src/SeqAn-1.3/seqan.h | 61 -
src/SeqAn-1.3/seqan/LICENSE | 26 -
src/SeqAn-1.3/seqan/align.h | 79 -
src/SeqAn-1.3/seqan/align/align_algorithms.h | 261 --
src/SeqAn-1.3/seqan/align/align_base.h | 656 ----
src/SeqAn-1.3/seqan/align/align_cols_base.h | 443 ---
src/SeqAn-1.3/seqan/align/align_dynprog.h | 578 ----
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src/SeqAn-1.3/seqan/align/align_hirschberg.h | 507 ---
src/SeqAn-1.3/seqan/align/align_iterator_base.h | 556 ----
src/SeqAn-1.3/seqan/align/align_local_dynprog.h | 881 -----
.../seqan/align/align_local_dynprog_banded.h | 585 ----
src/SeqAn-1.3/seqan/align/align_myers.h | 1041 ------
src/SeqAn-1.3/seqan/align/align_trace.h | 424 ---
src/SeqAn-1.3/seqan/align/gaps_array.h | 1184 -------
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src/SeqAn-1.3/seqan/align/hirschberg_set.h | 223 --
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src/SeqAn-1.3/seqan/basic/basic_allocator_to_std.h | 190 --
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src/SeqAn-1.3/seqan/basic/basic_alphabet_simple.h | 2357 -------------
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src/SeqAn-1.3/seqan/basic/basic_debug.h | 427 ---
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src/SeqAn-1.3/seqan/basic/basic_holder_dynamic.h | 210 --
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src/SeqAn-1.3/seqan/basic/basic_iterator.h | 805 -----
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src/SeqAn-1.3/seqan/basic/basic_proxy.h | 632 ----
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src/SeqAn-1.3/seqan/chaining/score_chain_sop.h | 248 --
src/SeqAn-1.3/seqan/chaining/score_manhattan.h | 188 --
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src/SeqAn-1.3/seqan/chaining/skip_base_element.h | 888 -----
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src/SeqAn-1.3/seqan/chaining/skip_list_dynamic.h | 468 ---
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src/SeqAn-1.3/seqan/chaining/skip_list_type.h | 391 ---
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src/SeqAn-1.3/seqan/misc/misc_cmdparser.h | 1722 ----------
src/SeqAn-1.3/seqan/misc/misc_dequeue.h | 369 ---
src/SeqAn-1.3/seqan/misc/misc_generated_forwards.h | 1123 -------
src/SeqAn-1.3/seqan/misc/misc_interval_tree.h | 1715 ----------
src/SeqAn-1.3/seqan/misc/misc_long_word.h | 850 -----
src/SeqAn-1.3/seqan/misc/misc_map.h | 218 --
src/SeqAn-1.3/seqan/misc/misc_parsing.h | 622 ----
src/SeqAn-1.3/seqan/misc/misc_random.h | 287 --
src/SeqAn-1.3/seqan/misc/misc_set.h | 613 ----
src/SeqAn-1.3/seqan/misc/misc_svg.h | 470 ---
src/SeqAn-1.3/seqan/misc/priority_type_base.h | 82 -
src/SeqAn-1.3/seqan/misc/priority_type_heap.h | 357 --
src/SeqAn-1.3/seqan/modifier.h | 70 -
src/SeqAn-1.3/seqan/modifier/modifier_alphabet.h | 774 -----
.../seqan/modifier/modifier_alphabet_expansion.h | 494 ---
src/SeqAn-1.3/seqan/modifier/modifier_functors.h | 228 --
.../seqan/modifier/modifier_generated_forwards.h | 717 ----
src/SeqAn-1.3/seqan/modifier/modifier_iterator.h | 706 ----
src/SeqAn-1.3/seqan/modifier/modifier_reverse.h | 628 ----
src/SeqAn-1.3/seqan/modifier/modifier_shortcuts.h | 516 ---
src/SeqAn-1.3/seqan/modifier/modifier_string.h | 653 ----
src/SeqAn-1.3/seqan/modifier/modifier_view.h | 420 ---
src/SeqAn-1.3/seqan/parallel.h | 58 -
.../seqan/parallel/parallel_atomic_misc.h | 116 -
.../seqan/parallel/parallel_atomic_primitives.h | 291 --
.../seqan/parallel/parallel_generated_forwards.h | 55 -
src/SeqAn-1.3/seqan/parallel/parallel_macros.h | 59 -
src/SeqAn-1.3/seqan/pipe.h | 83 -
src/SeqAn-1.3/seqan/pipe/pipe_base.h | 857 -----
src/SeqAn-1.3/seqan/pipe/pipe_caster.h | 110 -
src/SeqAn-1.3/seqan/pipe/pipe_counter.h | 106 -
src/SeqAn-1.3/seqan/pipe/pipe_echoer.h | 154 -
src/SeqAn-1.3/seqan/pipe/pipe_edit_environment.h | 348 --
src/SeqAn-1.3/seqan/pipe/pipe_filter.h | 121 -
src/SeqAn-1.3/seqan/pipe/pipe_generated_forwards.h | 738 -----
src/SeqAn-1.3/seqan/pipe/pipe_iterator.h | 264 --
src/SeqAn-1.3/seqan/pipe/pipe_joiner.h | 130 -
src/SeqAn-1.3/seqan/pipe/pipe_namer.h | 138 -
src/SeqAn-1.3/seqan/pipe/pipe_sampler.h | 540 ---
src/SeqAn-1.3/seqan/pipe/pipe_shifter.h | 167 -
src/SeqAn-1.3/seqan/pipe/pipe_source.h | 408 ---
src/SeqAn-1.3/seqan/pipe/pipe_tupler.h | 507 ---
src/SeqAn-1.3/seqan/pipe/pool_base.h | 1262 -------
src/SeqAn-1.3/seqan/pipe/pool_mapper.h | 697 ----
src/SeqAn-1.3/seqan/pipe/pool_sorter.h | 479 ---
src/SeqAn-1.3/seqan/platform.h | 46 -
src/SeqAn-1.3/seqan/platform/platform_gcc.h | 86 -
.../seqan/platform/platform_generated_forwards.h | 55 -
src/SeqAn-1.3/seqan/platform/platform_mingw.h | 65 -
src/SeqAn-1.3/seqan/platform/platform_solaris.h | 58 -
src/SeqAn-1.3/seqan/platform/platform_windows.h | 81 -
src/SeqAn-1.3/seqan/random.h | 70 -
src/SeqAn-1.3/seqan/random/ext_MersenneTwister.h | 468 ---
src/SeqAn-1.3/seqan/random/random_base.h | 155 -
.../seqan/random/random_generated_forwards.h | 251 --
src/SeqAn-1.3/seqan/random/random_geometric.h | 129 -
src/SeqAn-1.3/seqan/random/random_lognormal.h | 157 -
src/SeqAn-1.3/seqan/random/random_mt19937.h | 120 -
src/SeqAn-1.3/seqan/random/random_normal.h | 134 -
src/SeqAn-1.3/seqan/random/random_rng_functor.h | 127 -
src/SeqAn-1.3/seqan/random/random_shuffle.h | 88 -
src/SeqAn-1.3/seqan/random/random_uniform.h | 147 -
src/SeqAn-1.3/seqan/refinement.h | 67 -
.../refinement/graph_algorithm_refine_align.h | 186 --
.../refinement/graph_algorithm_refine_aligngraph.h | 292 --
.../refinement/graph_algorithm_refine_annotation.h | 396 ---
.../refinement/graph_algorithm_refine_exact.h | 567 ----
.../graph_algorithm_refine_exact_iterative.h | 666 ----
.../refinement/graph_algorithm_refine_fragment.h | 208 --
.../refinement/graph_algorithm_refine_inexact.h | 300 --
.../refinement/graph_algorithm_refine_scoring.h | 63 -
src/SeqAn-1.3/seqan/refinement/graph_impl_align.h | 2079 ------------
.../seqan/refinement/graph_impl_align_adapt.h | 425 ---
.../refinement/refinement_generated_forwards.h | 568 ----
src/SeqAn-1.3/seqan/score.h | 52 -
src/SeqAn-1.3/seqan/score/score_base.h | 211 --
src/SeqAn-1.3/seqan/score/score_edit.h | 142 -
.../seqan/score/score_generated_forwards.h | 350 --
src/SeqAn-1.3/seqan/score/score_matrix.h | 602 ----
src/SeqAn-1.3/seqan/score/score_matrix_data.h | 692 ----
src/SeqAn-1.3/seqan/score/score_simple.h | 372 ---
src/SeqAn-1.3/seqan/seeds.h | 64 -
src/SeqAn-1.3/seqan/seeds/banded_align.h | 711 ----
src/SeqAn-1.3/seqan/seeds/banded_chain_align.h | 1310 --------
.../seqan/seeds/banded_chain_align_affine.h | 1680 ----------
src/SeqAn-1.3/seqan/seeds/global_seed_chain.h | 306 --
src/SeqAn-1.3/seqan/seeds/memoryManager_base.h | 389 ---
src/SeqAn-1.3/seqan/seeds/memoryManager_int.h | 337 --
src/SeqAn-1.3/seqan/seeds/propertyMap.h | 239 --
src/SeqAn-1.3/seqan/seeds/seedHandlingTags.h | 168 -
src/SeqAn-1.3/seqan/seeds/seedSet_base.h | 1691 ----------
src/SeqAn-1.3/seqan/seeds/seedSet_iterator.h | 316 --
src/SeqAn-1.3/seqan/seeds/seedSet_score.h | 2136 ------------
src/SeqAn-1.3/seqan/seeds/seed_base.h | 1089 ------
src/SeqAn-1.3/seqan/seeds/seed_multi.h | 755 -----
.../seqan/seeds/seeds_generated_forwards.h | 860 -----
src/SeqAn-1.3/seqan/seeds2.h | 96 -
src/SeqAn-1.3/seqan/seeds2/align_chain_banded.h | 828 -----
src/SeqAn-1.3/seqan/seeds2/align_dynprog_affine.h | 516 ---
.../seqan/seeds2/align_dynprog_banded_affine.h | 563 ----
.../seqan/seeds2/align_dynprog_banded_linear.h | 495 ---
src/SeqAn-1.3/seqan/seeds2/align_dynprog_linear.h | 461 ---
src/SeqAn-1.3/seqan/seeds2/basic_iter_indirect.h | 171 -
.../seqan/seeds2/seeds2_generated_forwards.h | 747 -----
src/SeqAn-1.3/seqan/seeds2/seeds_base.h | 42 -
src/SeqAn-1.3/seqan/seeds2/seeds_combination.h | 464 ---
src/SeqAn-1.3/seqan/seeds2/seeds_extension.h | 735 -----
src/SeqAn-1.3/seqan/seeds2/seeds_global_chaining.h | 258 --
.../seqan/seeds2/seeds_global_chaining_base.h | 44 -
.../seqan/seeds2/seeds_global_chaining_gusfield.h | 48 -
src/SeqAn-1.3/seqan/seeds2/seeds_seed_base.h | 570 ----
src/SeqAn-1.3/seqan/seeds2/seeds_seed_chained.h | 419 ---
src/SeqAn-1.3/seqan/seeds2/seeds_seed_diagonal.h | 130 -
src/SeqAn-1.3/seqan/seeds2/seeds_seed_set_base.h | 283 --
.../seqan/seeds2/seeds_seed_set_non_scored.h | 69 -
src/SeqAn-1.3/seqan/seeds2/seeds_seed_set_scored.h | 69 -
.../seqan/seeds2/seeds_seed_set_unordered.h | 384 ---
src/SeqAn-1.3/seqan/seeds2/seeds_seed_simple.h | 328 --
src/SeqAn-1.3/seqan/sequence.h | 114 -
src/SeqAn-1.3/seqan/sequence/adapt_array_pointer.h | 837 -----
src/SeqAn-1.3/seqan/sequence/adapt_std_list.h | 300 --
src/SeqAn-1.3/seqan/sequence/adapt_std_string.h | 693 ----
src/SeqAn-1.3/seqan/sequence/adapt_std_vector.h | 708 ----
src/SeqAn-1.3/seqan/sequence/iter_concat_virtual.h | 516 ---
src/SeqAn-1.3/seqan/sequence/segment_base.h | 1358 --------
src/SeqAn-1.3/seqan/sequence/segment_infix.h | 900 -----
src/SeqAn-1.3/seqan/sequence/segment_prefix.h | 748 -----
src/SeqAn-1.3/seqan/sequence/segment_suffix.h | 744 -----
.../seqan/sequence/sequence_concatenator.h | 255 --
src/SeqAn-1.3/seqan/sequence/sequence_forwards.h | 84 -
.../seqan/sequence/sequence_generated_forwards.h | 2138 ------------
src/SeqAn-1.3/seqan/sequence/sequence_interface.h | 1700 ----------
src/SeqAn-1.3/seqan/sequence/sequence_lexical.h | 833 -----
src/SeqAn-1.3/seqan/sequence/sequence_shortcuts.h | 271 --
src/SeqAn-1.3/seqan/sequence/sequence_stream.h | 170 -
src/SeqAn-1.3/seqan/sequence/string_alloc.h | 438 ---
src/SeqAn-1.3/seqan/sequence/string_array.h | 288 --
src/SeqAn-1.3/seqan/sequence/string_base.h | 1948 -----------
src/SeqAn-1.3/seqan/sequence/string_block.h | 615 ----
src/SeqAn-1.3/seqan/sequence/string_cstyle.h | 943 ------
src/SeqAn-1.3/seqan/sequence/string_packed.h | 1335 --------
src/SeqAn-1.3/seqan/sequence/string_set_base.h | 1411 --------
.../seqan/sequence/string_set_concat_direct.h | 469 ---
.../seqan/sequence/string_set_dependent_generous.h | 262 --
.../seqan/sequence/string_set_dependent_tight.h | 322 --
src/SeqAn-1.3/seqan/sequence/string_set_owner.h | 283 --
src/SeqAn-1.3/seqan/sequence_journaled.h | 81 -
.../journal_entries_sorted_array.h | 476 ---
.../journal_entries_unbalanced_tree.h | 695 ----
.../journal_entries_unbalanced_tree_iterator.h | 528 ---
.../journal_entries_unbalanced_tree_node.h | 145 -
.../seqan/sequence_journaled/journal_entry.h | 144 -
.../seqan/sequence_journaled/sequence_journaled.h | 536 ---
.../sequence_journaled_forwards.h | 51 -
.../sequence_journaled_generated_forwards.h | 440 ---
.../sequence_journaled_iterator.h | 480 ---
src/SeqAn-1.3/seqan/statistics.h | 53 -
src/SeqAn-1.3/seqan/statistics/statistics_base.h | 501 ---
.../statistics/statistics_generated_forwards.h | 182 --
.../seqan/statistics/statistics_markov_model.h | 834 -----
src/SeqAn-1.3/seqan/store.h | 78 -
src/SeqAn-1.3/seqan/store/store_align.h | 1932 -----------
src/SeqAn-1.3/seqan/store/store_align_intervals.h | 357 --
src/SeqAn-1.3/seqan/store/store_all.h | 2004 ------------
src/SeqAn-1.3/seqan/store/store_annotation.h | 705 ----
src/SeqAn-1.3/seqan/store/store_base.h | 282 --
src/SeqAn-1.3/seqan/store/store_contig.h | 205 --
.../seqan/store/store_generated_forwards.h | 1276 --------
src/SeqAn-1.3/seqan/store/store_intervaltree.h | 197 --
src/SeqAn-1.3/seqan/store/store_io.h | 1213 -------
src/SeqAn-1.3/seqan/store/store_io_bam.h | 572 ----
src/SeqAn-1.3/seqan/store/store_io_gff.h | 735 -----
src/SeqAn-1.3/seqan/store/store_io_sam.h | 1133 -------
src/SeqAn-1.3/seqan/store/store_io_ucsc.h | 601 ----
src/SeqAn-1.3/seqan/store/store_library.h | 94 -
src/SeqAn-1.3/seqan/store/store_matepair.h | 112 -
src/SeqAn-1.3/seqan/store/store_read.h | 101 -
src/SeqAn-1.3/seqan/system.h | 93 -
src/SeqAn-1.3/seqan/system/file_async.h | 1035 ------
src/SeqAn-1.3/seqan/system/file_directory.h | 284 --
src/SeqAn-1.3/seqan/system/file_manual_forwards.h | 160 -
src/SeqAn-1.3/seqan/system/file_sync.h | 421 ---
src/SeqAn-1.3/seqan/system/system_base.h | 65 -
src/SeqAn-1.3/seqan/system/system_event.h | 315 --
.../seqan/system/system_generated_forwards.h | 55 -
.../seqan/system/system_manual_forwards.h | 124 -
src/SeqAn-1.3/seqan/system/system_mutex.h | 183 --
src/SeqAn-1.3/seqan/system/system_sema.h | 149 -
src/SeqAn-1.3/seqan/system/system_thread.h | 215 --
508 files changed, 256841 deletions(-)
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