[med-svn] [tophat] branch master updated (b9f9ebc -> f4cf751)
Andreas Tille
tille at debian.org
Tue Mar 18 13:17:01 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository tophat.
from b9f9ebc Move debian/upstream to debian/upstream/metadata
new 3f76311 New upstream version
adds b2fc8e4 Imported Upstream version 2.0.10
new 2770873 Imported Upstream version 2.0.11
new 99e71ac Merge tag 'upstream/2.0.11'
new 029172f cme fix dpkg-control
new f4cf751 New upstream version fixes Build problem
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
configure | 24 +-
configure.ac | 2 +-
debian/changelog | 8 +-
debian/control | 33 +-
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 +-
514 files changed, 256911 insertions(+), 54 deletions(-)
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create mode 100644 src/SeqAn-1.3/seqan/LICENSE
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