This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository tophat.
commit 99e71ac31a3a4f8baceb69608d86c57c03252915 Merge: 3f76311 2770873 Author: Andreas Tille <[email protected]> Date: Tue Mar 18 13:58:19 2014 +0100 Merge tag 'upstream/2.0.11' Upstream version 2.0.11 configure | 24 +- configure.ac | 2 +- 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 ++++ .../seqan/align/align_generated_forwards.h | 1158 +++++++ 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 +++++++ src/SeqAn-1.3/seqan/align/gaps_base.h | 1335 ++++++++ src/SeqAn-1.3/seqan/align/gaps_iterator_base.h | 323 ++ src/SeqAn-1.3/seqan/align/gaps_sumlist.h | 938 ++++++ src/SeqAn-1.3/seqan/align/hirschberg_set.h | 223 ++ src/SeqAn-1.3/seqan/align/matrix_base.h | 1106 +++++++ src/SeqAn-1.3/seqan/basic.h | 142 + src/SeqAn-1.3/seqan/basic/basic_aggregates.h | 732 +++++ .../seqan/basic/basic_allocator_chunkpool.h | 335 ++ .../seqan/basic/basic_allocator_interface.h | 307 ++ .../seqan/basic/basic_allocator_multipool.h | 243 ++ src/SeqAn-1.3/seqan/basic/basic_allocator_simple.h | 224 ++ .../seqan/basic/basic_allocator_singlepool.h | 312 ++ src/SeqAn-1.3/seqan/basic/basic_allocator_to_std.h | 190 ++ .../seqan/basic/basic_alphabet_interface.h | 1104 +++++++ .../seqan/basic/basic_alphabet_interface2.h | 246 ++ src/SeqAn-1.3/seqan/basic/basic_alphabet_simple.h | 2357 +++++++++++++ .../seqan/basic/basic_alphabet_simple_tabs.h | 595 ++++ .../seqan/basic/basic_alphabet_trait_basic.h | 772 +++++ src/SeqAn-1.3/seqan/basic/basic_compare.h | 74 + src/SeqAn-1.3/seqan/basic/basic_converter.h | 128 + src/SeqAn-1.3/seqan/basic/basic_counted_ptr.h | 128 + src/SeqAn-1.3/seqan/basic/basic_debug.h | 427 +++ src/SeqAn-1.3/seqan/basic/basic_definition.h | 429 +++ src/SeqAn-1.3/seqan/basic/basic_forwards.h | 81 + .../seqan/basic/basic_generated_forwards.h | 2403 ++++++++++++++ src/SeqAn-1.3/seqan/basic/basic_holder.h | 1638 ++++++++++ src/SeqAn-1.3/seqan/basic/basic_holder_dynamic.h | 210 ++ src/SeqAn-1.3/seqan/basic/basic_host.h | 183 ++ src/SeqAn-1.3/seqan/basic/basic_iterator.h | 805 +++++ .../seqan/basic/basic_iterator_adapt_std.h | 449 +++ src/SeqAn-1.3/seqan/basic/basic_iterator_adaptor.h | 587 ++++ src/SeqAn-1.3/seqan/basic/basic_iterator_base.h | 349 ++ .../seqan/basic/basic_iterator_position.h | 479 +++ src/SeqAn-1.3/seqan/basic/basic_iterator_simple.h | 130 + src/SeqAn-1.3/seqan/basic/basic_logvalue.h | 330 ++ src/SeqAn-1.3/seqan/basic/basic_metaprogramming.h | 361 ++ src/SeqAn-1.3/seqan/basic/basic_operator.h | 44 + src/SeqAn-1.3/seqan/basic/basic_parallelism.h | 64 + src/SeqAn-1.3/seqan/basic/basic_pointer.h | 115 + src/SeqAn-1.3/seqan/basic/basic_profchar.h | 213 ++ src/SeqAn-1.3/seqan/basic/basic_profile.h | 552 ++++ src/SeqAn-1.3/seqan/basic/basic_proxy.h | 632 ++++ src/SeqAn-1.3/seqan/basic/basic_sse2.h | 506 +++ src/SeqAn-1.3/seqan/basic/basic_tag.h | 251 ++ src/SeqAn-1.3/seqan/basic/basic_testing.h | 1687 ++++++++++ src/SeqAn-1.3/seqan/basic/basic_transport.h | 209 ++ src/SeqAn-1.3/seqan/basic/basic_type.h | 710 ++++ src/SeqAn-1.3/seqan/basic/basic_volatile_ptr.h | 171 + src/SeqAn-1.3/seqan/blast.h | 72 + src/SeqAn-1.3/seqan/blast/blast_base.h | 197 ++ .../seqan/blast/blast_generated_forwards.h | 807 +++++ src/SeqAn-1.3/seqan/blast/blast_hit.h | 306 ++ src/SeqAn-1.3/seqan/blast/blast_hit_iterator.h | 441 +++ src/SeqAn-1.3/seqan/blast/blast_hsp.h | 1696 ++++++++++ src/SeqAn-1.3/seqan/blast/blast_hsp_iterator.h | 310 ++ src/SeqAn-1.3/seqan/blast/blast_iterator.h | 69 + src/SeqAn-1.3/seqan/blast/blast_parsing.h | 137 + src/SeqAn-1.3/seqan/blast/blast_report.h | 1170 +++++++ src/SeqAn-1.3/seqan/blast/blast_run.h | 418 +++ src/SeqAn-1.3/seqan/blast/blast_stream_hit.h | 135 + .../seqan/blast/blast_stream_hit_iterator.h | 453 +++ .../seqan/blast/blast_stream_hsp_iterator.h | 435 +++ src/SeqAn-1.3/seqan/blast/blast_stream_report.h | 241 ++ src/SeqAn-1.3/seqan/chaining.h | 75 + src/SeqAn-1.3/seqan/chaining/chain_base.h | 371 +++ src/SeqAn-1.3/seqan/chaining/chain_generic.h | 260 ++ src/SeqAn-1.3/seqan/chaining/chain_meta_fragment.h | 204 ++ src/SeqAn-1.3/seqan/chaining/chain_point.h | 497 +++ src/SeqAn-1.3/seqan/chaining/chain_wrapper_point.h | 241 ++ .../seqan/chaining/chaining_generated_forwards.h | 1515 +++++++++ src/SeqAn-1.3/seqan/chaining/fragment.h | 402 +++ src/SeqAn-1.3/seqan/chaining/geom_distribution.h | 75 + src/SeqAn-1.3/seqan/chaining/range_max_tree.h | 52 + src/SeqAn-1.3/seqan/chaining/range_tree.h | 58 + src/SeqAn-1.3/seqan/chaining/rmt_base.h | 310 ++ src/SeqAn-1.3/seqan/chaining/rmt_common_algos.h | 329 ++ src/SeqAn-1.3/seqan/chaining/rmt_compl_algos.h | 282 ++ src/SeqAn-1.3/seqan/chaining/rmt_def_algos.h | 119 + .../seqan/chaining/rmt_skip_base_element.h | 59 + src/SeqAn-1.3/seqan/chaining/rmt_skip_element.h | 126 + src/SeqAn-1.3/seqan/chaining/rt_base.h | 345 ++ src/SeqAn-1.3/seqan/chaining/rt_common_algos.h | 212 ++ src/SeqAn-1.3/seqan/chaining/rt_impl.h | 162 + .../seqan/chaining/rt_skip_base_element.h | 72 + src/SeqAn-1.3/seqan/chaining/rt_skip_element.h | 244 ++ src/SeqAn-1.3/seqan/chaining/rt_sl_base.h | 368 +++ src/SeqAn-1.3/seqan/chaining/rt_sl_compl_algos.h | 164 + src/SeqAn-1.3/seqan/chaining/rt_sl_def_algos.h | 144 + src/SeqAn-1.3/seqan/chaining/rt_sl_impl.h | 243 ++ src/SeqAn-1.3/seqan/chaining/score_chain.h | 54 + src/SeqAn-1.3/seqan/chaining/score_chain_sop.h | 248 ++ src/SeqAn-1.3/seqan/chaining/score_manhattan.h | 188 ++ src/SeqAn-1.3/seqan/chaining/score_zero.h | 152 + src/SeqAn-1.3/seqan/chaining/skip_base_element.h | 888 +++++ src/SeqAn-1.3/seqan/chaining/skip_element.h | 457 +++ src/SeqAn-1.3/seqan/chaining/skip_list.h | 69 + src/SeqAn-1.3/seqan/chaining/skip_list_base.h | 1016 ++++++ src/SeqAn-1.3/seqan/chaining/skip_list_dynamic.h | 468 +++ src/SeqAn-1.3/seqan/chaining/skip_list_impl.h | 701 ++++ src/SeqAn-1.3/seqan/chaining/skip_list_iterator.h | 279 ++ src/SeqAn-1.3/seqan/chaining/skip_list_type.h | 391 +++ src/SeqAn-1.3/seqan/chaining/skip_pool_alloc.h | 377 +++ src/SeqAn-1.3/seqan/chaining/tree_chain.h | 130 + src/SeqAn-1.3/seqan/chaining/tree_chain_sop.h | 202 ++ src/SeqAn-1.3/seqan/chaining/tree_chain_utils.h | 567 ++++ src/SeqAn-1.3/seqan/consensus.h | 57 + src/SeqAn-1.3/seqan/consensus/consensus_base.h | 1806 ++++++++++ .../seqan/consensus/consensus_generated_forwards.h | 304 ++ src/SeqAn-1.3/seqan/consensus/consensus_library.h | 580 ++++ src/SeqAn-1.3/seqan/consensus/consensus_realign.h | 763 +++++ src/SeqAn-1.3/seqan/consensus/consensus_score.h | 388 +++ src/SeqAn-1.3/seqan/file.h | 113 + src/SeqAn-1.3/seqan/file/chunk_collector.h | 554 ++++ src/SeqAn-1.3/seqan/file/cstream.h | 307 ++ src/SeqAn-1.3/seqan/file/file_array.h | 439 +++ src/SeqAn-1.3/seqan/file/file_base.h | 759 +++++ src/SeqAn-1.3/seqan/file/file_cstyle.h | 245 ++ src/SeqAn-1.3/seqan/file/file_filereader.h | 954 ++++++ src/SeqAn-1.3/seqan/file/file_filereaderiterator.h | 157 + src/SeqAn-1.3/seqan/file/file_format.h | 705 ++++ src/SeqAn-1.3/seqan/file/file_format_cgviz.h | 240 ++ src/SeqAn-1.3/seqan/file/file_format_embl.h | 639 ++++ src/SeqAn-1.3/seqan/file/file_format_fasta.h | 587 ++++ src/SeqAn-1.3/seqan/file/file_format_fasta_align.h | 339 ++ src/SeqAn-1.3/seqan/file/file_format_genbank.h | 381 +++ src/SeqAn-1.3/seqan/file/file_format_guess.h | 116 + src/SeqAn-1.3/seqan/file/file_format_mmap.h | 1372 ++++++++ src/SeqAn-1.3/seqan/file/file_format_raw.h | 319 ++ src/SeqAn-1.3/seqan/file/file_forwards.h | 56 + src/SeqAn-1.3/seqan/file/file_generated_forwards.h | 1371 ++++++++ src/SeqAn-1.3/seqan/file/file_page.h | 1093 +++++++ src/SeqAn-1.3/seqan/file/file_page_raid0.h | 209 ++ src/SeqAn-1.3/seqan/file/meta.h | 48 + src/SeqAn-1.3/seqan/file/stream.h | 446 +++ src/SeqAn-1.3/seqan/file/stream_algorithms.h | 221 ++ src/SeqAn-1.3/seqan/file/string_external.h | 2081 ++++++++++++ src/SeqAn-1.3/seqan/file/string_mmap.h | 832 +++++ src/SeqAn-1.3/seqan/find.h | 95 + src/SeqAn-1.3/seqan/find/find_abndm.h | 639 ++++ src/SeqAn-1.3/seqan/find/find_ahocorasick.h | 323 ++ src/SeqAn-1.3/seqan/find/find_base.h | 885 +++++ src/SeqAn-1.3/seqan/find/find_begin.h | 395 +++ src/SeqAn-1.3/seqan/find/find_bndm.h | 261 ++ src/SeqAn-1.3/seqan/find/find_bom.h | 242 ++ src/SeqAn-1.3/seqan/find/find_generated_forwards.h | 1062 ++++++ src/SeqAn-1.3/seqan/find/find_hamming_simple.h | 272 ++ src/SeqAn-1.3/seqan/find/find_horspool.h | 476 +++ src/SeqAn-1.3/seqan/find/find_multi.h | 160 + src/SeqAn-1.3/seqan/find/find_multiple_bfam.h | 401 +++ src/SeqAn-1.3/seqan/find/find_multiple_shiftand.h | 436 +++ src/SeqAn-1.3/seqan/find/find_myers_ukkonen.h | 1677 ++++++++++ src/SeqAn-1.3/seqan/find/find_pattern_base.h | 398 +++ src/SeqAn-1.3/seqan/find/find_pex.h | 726 ++++ src/SeqAn-1.3/seqan/find/find_score.h | 500 +++ src/SeqAn-1.3/seqan/find/find_set_horspool.h | 301 ++ src/SeqAn-1.3/seqan/find/find_shiftand.h | 297 ++ src/SeqAn-1.3/seqan/find/find_shiftor.h | 332 ++ src/SeqAn-1.3/seqan/find/find_simple.h | 162 + src/SeqAn-1.3/seqan/find/find_wild_shiftand.h | 689 ++++ src/SeqAn-1.3/seqan/find/find_wumanber.h | 482 +++ src/SeqAn-1.3/seqan/find2.h | 79 + .../seqan/find2/find2_generated_forwards.h | 477 +++ src/SeqAn-1.3/seqan/find2/find_approx_dpsearch.h | 603 ++++ src/SeqAn-1.3/seqan/find2/find_approx_find_begin.h | 223 ++ src/SeqAn-1.3/seqan/find2/find_base.h | 83 + src/SeqAn-1.3/seqan/find2/find_exact_shiftand.h | 495 +++ src/SeqAn-1.3/seqan/find2/find_exact_simple.h | 346 ++ src/SeqAn-1.3/seqan/find2/find_finder_default.h | 157 + src/SeqAn-1.3/seqan/find2/find_hamming_simple.h | 384 +++ .../seqan/find2/find_multiple_exact_simple.h | 473 +++ .../seqan/find2/find_pattern_wild_shiftand.h | 874 +++++ src/SeqAn-1.3/seqan/find_motif.h | 75 + src/SeqAn-1.3/seqan/find_motif/em_algorithm.h | 870 +++++ src/SeqAn-1.3/seqan/find_motif/find_motif_base.h | 366 +++ .../find_motif/find_motif_epatternbranching.h | 768 +++++ .../find_motif/find_motif_generated_forwards.h | 472 +++ src/SeqAn-1.3/seqan/find_motif/find_motif_pms1.h | 822 +++++ src/SeqAn-1.3/seqan/find_motif/find_motif_pmsp.h | 792 +++++ .../seqan/find_motif/find_motif_projection.h | 1256 +++++++ .../seqan/find_motif/frequency_distribution.h | 641 ++++ src/SeqAn-1.3/seqan/find_motif/profile.h | 242 ++ src/SeqAn-1.3/seqan/find_motif/pseudocount_base.h | 80 + .../seqan/find_motif/pseudocount_mode_c.h | 165 + .../seqan/find_motif/pseudocount_mode_p.h | 165 + .../seqan/find_motif/sequence_model_types.h | 136 + src/SeqAn-1.3/seqan/graph_algorithms.h | 55 + .../seqan/graph_algorithms/graph_algorithm.h | 1991 +++++++++++ .../graph_algorithms/graph_algorithm_heap_tree.h | 514 +++ .../seqan/graph_algorithms/graph_algorithm_hmm.h | 1162 +++++++ .../graph_algorithms/graph_algorithm_lis_his.h | 405 +++ .../graph_algorithms_generated_forwards.h | 424 +++ src/SeqAn-1.3/seqan/graph_align.h | 59 + .../seqan/graph_align/graph_align_banded_gotoh.h | 348 ++ .../graph_align_banded_needleman_wunsch.h | 508 +++ .../graph_align_banded_smith_waterman_clump.h | 356 ++ src/SeqAn-1.3/seqan/graph_align/graph_align_base.h | 280 ++ .../seqan/graph_align/graph_align_config.h | 571 ++++ .../graph_align/graph_align_generated_forwards.h | 327 ++ .../seqan/graph_align/graph_align_gotoh.h | 327 ++ .../seqan/graph_align/graph_align_hirschberg.h | 529 +++ .../seqan/graph_align/graph_align_interface.h | 454 +++ .../graph_align/graph_align_needleman_wunsch.h | 288 ++ .../seqan/graph_align/graph_align_smith_waterman.h | 388 +++ .../graph_align/graph_align_smith_waterman_clump.h | 125 + src/SeqAn-1.3/seqan/graph_msa.h | 59 + .../seqan/graph_msa/graph_align_tcoffee_base.h | 1050 ++++++ .../seqan/graph_msa/graph_align_tcoffee_distance.h | 222 ++ .../graph_msa/graph_align_tcoffee_guidetree.h | 882 +++++ .../seqan/graph_msa/graph_align_tcoffee_io.h | 1042 ++++++ .../seqan/graph_msa/graph_align_tcoffee_kmer.h | 153 + .../seqan/graph_msa/graph_align_tcoffee_library.h | 544 +++ .../seqan/graph_msa/graph_align_tcoffee_msa.h | 483 +++ .../graph_msa/graph_align_tcoffee_progressive.h | 489 +++ .../graph_msa/graph_align_tcoffee_refinement.h | 515 +++ .../seqan/graph_msa/graph_msa_generated_forwards.h | 541 +++ src/SeqAn-1.3/seqan/graph_types.h | 89 + src/SeqAn-1.3/seqan/graph_types/graph_base.h | 285 ++ src/SeqAn-1.3/seqan/graph_types/graph_drawing.h | 937 ++++++ src/SeqAn-1.3/seqan/graph_types/graph_edgestump.h | 1046 ++++++ src/SeqAn-1.3/seqan/graph_types/graph_idmanager.h | 480 +++ .../seqan/graph_types/graph_impl_automaton.h | 1008 ++++++ .../seqan/graph_types/graph_impl_directed.h | 1010 ++++++ .../seqan/graph_types/graph_impl_fragment.h | 452 +++ src/SeqAn-1.3/seqan/graph_types/graph_impl_hmm.h | 1051 ++++++ .../seqan/graph_types/graph_impl_oracle.h | 265 ++ src/SeqAn-1.3/seqan/graph_types/graph_impl_tree.h | 1101 +++++++ src/SeqAn-1.3/seqan/graph_types/graph_impl_trie.h | 275 ++ .../seqan/graph_types/graph_impl_undirected.h | 819 +++++ .../seqan/graph_types/graph_impl_wordgraph.h | 287 ++ src/SeqAn-1.3/seqan/graph_types/graph_interface.h | 465 +++ src/SeqAn-1.3/seqan/graph_types/graph_iterator.h | 97 + .../seqan/graph_types/graph_iterator_adjacency.h | 346 ++ .../seqan/graph_types/graph_iterator_bfs.h | 302 ++ .../seqan/graph_types/graph_iterator_dfs.h | 305 ++ .../seqan/graph_types/graph_iterator_edge.h | 481 +++ .../seqan/graph_types/graph_iterator_outedge.h | 1225 +++++++ .../seqan/graph_types/graph_iterator_vertex.h | 473 +++ src/SeqAn-1.3/seqan/graph_types/graph_property.h | 759 +++++ .../graph_types/graph_types_generated_forwards.h | 1374 ++++++++ .../seqan/graph_types/graph_utility_parsing.h | 90 + src/SeqAn-1.3/seqan/index.h | 162 + src/SeqAn-1.3/seqan/index/find_index.h | 312 ++ src/SeqAn-1.3/seqan/index/find_index_approx.h | 229 ++ src/SeqAn-1.3/seqan/index/find_index_esa.h | 1944 +++++++++++ src/SeqAn-1.3/seqan/index/find_index_qgram.h | 97 + src/SeqAn-1.3/seqan/index/find_quasar.h | 167 + src/SeqAn-1.3/seqan/index/find_swift.h | 1956 +++++++++++ src/SeqAn-1.3/seqan/index/index_base.h | 1181 +++++++ src/SeqAn-1.3/seqan/index/index_bwt.h | 313 ++ src/SeqAn-1.3/seqan/index/index_childtab.h | 328 ++ src/SeqAn-1.3/seqan/index/index_dfi.h | 599 ++++ src/SeqAn-1.3/seqan/index/index_esa_algs.h | 1010 ++++++ src/SeqAn-1.3/seqan/index/index_esa_algs_multi.h | 720 ++++ src/SeqAn-1.3/seqan/index/index_esa_base.h | 434 +++ src/SeqAn-1.3/seqan/index/index_esa_drawing.h | 108 + src/SeqAn-1.3/seqan/index/index_esa_stree.h | 2288 +++++++++++++ .../seqan/index/index_generated_forwards.h | 3450 ++++++++++++++++++++ src/SeqAn-1.3/seqan/index/index_lcp.h | 531 +++ src/SeqAn-1.3/seqan/index/index_lcp_tree.h | 178 + src/SeqAn-1.3/seqan/index/index_manual_forwards.h | 69 + src/SeqAn-1.3/seqan/index/index_pizzachili.h | 384 +++ src/SeqAn-1.3/seqan/index/index_pizzachili_find.h | 174 + .../seqan/index/index_pizzachili_string.h | 803 +++++ src/SeqAn-1.3/seqan/index/index_qgram.h | 2416 ++++++++++++++ .../seqan/index/index_qgram_openaddressing.h | 341 ++ src/SeqAn-1.3/seqan/index/index_sa_btree.h | 133 + src/SeqAn-1.3/seqan/index/index_sa_bwtwalk.h | 660 ++++ src/SeqAn-1.3/seqan/index/index_sa_lss.h | 451 +++ src/SeqAn-1.3/seqan/index/index_sa_mm.h | 201 ++ src/SeqAn-1.3/seqan/index/index_sa_qsort.h | 241 ++ src/SeqAn-1.3/seqan/index/index_shawarma.h | 93 + src/SeqAn-1.3/seqan/index/index_shims.h | 872 +++++ src/SeqAn-1.3/seqan/index/index_skew3.h | 544 +++ src/SeqAn-1.3/seqan/index/index_skew7.h | 853 +++++ src/SeqAn-1.3/seqan/index/index_skew7_multi.h | 424 +++ src/SeqAn-1.3/seqan/index/index_wotd.h | 1994 +++++++++++ src/SeqAn-1.3/seqan/index/pipe_merger3.h | 167 + src/SeqAn-1.3/seqan/index/pipe_merger7.h | 520 +++ src/SeqAn-1.3/seqan/index/pizzachili_api.h | 182 ++ src/SeqAn-1.3/seqan/index/pump_extender3.h | 136 + src/SeqAn-1.3/seqan/index/pump_extender7.h | 514 +++ src/SeqAn-1.3/seqan/index/pump_lcp_core.h | 391 +++ src/SeqAn-1.3/seqan/index/pump_separator7.h | 85 + src/SeqAn-1.3/seqan/index/radix.h | 195 ++ src/SeqAn-1.3/seqan/index/repeat_base.h | 325 ++ src/SeqAn-1.3/seqan/index/shape_base.h | 750 +++++ src/SeqAn-1.3/seqan/index/shape_gapped.h | 661 ++++ src/SeqAn-1.3/seqan/index/shape_onegapped.h | 376 +++ src/SeqAn-1.3/seqan/index/shape_predefined.h | 128 + src/SeqAn-1.3/seqan/index/shape_threshold.h | 1124 +++++++ src/SeqAn-1.3/seqan/map.h | 68 + src/SeqAn-1.3/seqan/map/map_adapter_stl.h | 753 +++++ src/SeqAn-1.3/seqan/map/map_base.h | 253 ++ src/SeqAn-1.3/seqan/map/map_chooser.h | 66 + src/SeqAn-1.3/seqan/map/map_generated_forwards.h | 581 ++++ src/SeqAn-1.3/seqan/map/map_skiplist.h | 1163 +++++++ src/SeqAn-1.3/seqan/map/map_vector.h | 512 +++ src/SeqAn-1.3/seqan/map/sumlist.h | 214 ++ src/SeqAn-1.3/seqan/map/sumlist_mini.h | 976 ++++++ src/SeqAn-1.3/seqan/map/sumlist_skip.h | 1124 +++++++ src/SeqAn-1.3/seqan/misc/edit_environment.h | 883 +++++ src/SeqAn-1.3/seqan/misc/misc_base.h | 124 + 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 ++ src/tophat-fusion-post | 55 +- src/tophat.py | 2 +- 512 files changed, 256884 insertions(+), 40 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
