[DOC] Fixing URL in README.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12471 e6417c60-b987-48fd-844e-b20f0fcc1017
[API,FEATURE] Large update to the align module.

 * More consistent interface to DP global, local, and declumping algorithms.
 * Merging of module graph_align into align.
 * New implementation of Array Gaps class.
 * Anchor Gaps class now lives in align.
 * More consistent implementation for clipping.
 * Clearer structure of align module.
 * Better API documentation of align module.
 * Integration of new align module with the rest of the libraries and apps (excluding snp_store).


git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12473 e6417c60-b987-48fd-844e-b20f0fcc1017
[API] Moving modules seq_io and bam_io from extras to core.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12478 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] Converting refinement module to new stream module.

Also adding test for dot drawing.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12479 e6417c60-b987-48fd-844e-b20f0fcc1017
[API,FEATURE] Adding `startsWith()` and `endsWith()` to module `sequence`.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12480 e6417c60-b987-48fd-844e-b20f0fcc1017
[API] Moving modules `sam_io` and `bam_io` from extras to core.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12481 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] ESA `.dot` output now uses new stream interface.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12482 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Adding missing `test_seq_io_generic.h`.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12483 e6417c60-b987-48fd-844e-b20f0fcc1017
[COMMENT] Removing old parsing functions that were commented out anyway.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12484 e6417c60-b987-48fd-844e-b20f0fcc1017
[TEST] Adding tests for alignments.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12485 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] Switching align module to new stream interface.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12486 e6417c60-b987-48fd-844e-b20f0fcc1017
[COMMENT] Removing superflous, commented out line.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12487 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] Removing superflous header ext_lh3.h

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12488 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] Modules find_motif, statistics, and blast do not need generated forwards any more.

Modified module find_motif a bit to allow for this.
Added some manual forwards and reordered some code in this module.


git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12489 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] No more checkpoint verification in extras tests.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12490 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Adjusting module misc and file to latest stream and I/O changes.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12491 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing CMakeLists.txt in extras/demos/tutorial.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12492 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Updating text boxes trac plugin, css classes for boxes.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12493 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Updating text_boxes CSS somewhat.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12494 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] Reordering code such that it compiles without generated forwards.

The changed modules are file, graph_algorithms, stream, refinement, modifier, map, find, sequence_journaled, seeds2, pipe, graph_msa, seeds, index, score, chaining, consensus, graph_types, map.

git-svn-id: http://svn.mi.fu-berlin.de/seqan/trunk/seqan@12495 e6417c60-b987-48fd-844e-b20f0fcc1017