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Staden Package release 2.0.0b9: 5th Dec 2011 ============================================ Firstly, it has been a long time since the last flagged release (February). Yes Gap5 is still in beta, but stability is improving fast. (Gap4 and co are largely unchanged so please consider them as production worthy, or download an older set of binaries.) Primarily work has revolved around bug-fixing, initially spurred on by the creation of a Check Database function and internally using a random simulated user for automatically doing all manner of edits and observing the stability and correctness of the results. Obviously bugs still exist, but we believe this is the most robust version of Gap5 to date. However during the year we have also added many new features, mostly driven by internal user requests, and improvements to existing features. (We are more than happy to receive ideas and feature requests from external users too.) Many of these are simply transported over from Gap4 (Shuffle Pads, Check Assembly, Restriction Enzyme Plot, Contigs to Readings, and so on), but some have been added to face the new challenges with NGS data typically caused by excessive depth (bulk clipping, Group Readings, depth searching). A summary of changes is visible below, but the on-going NEWS summary is visible within the subversion repository at: http://staden.svn.sourceforge.net/viewvc/staden/staden/trunk/src/NEWS James Bonfield & Andrew Whitwham Main Gap5 Updates ----------------- * Major overhaul of the consensus algorithm. It now allows for the possibility of SNPs when computing the consensus scores. Also added a discrepancy calculation where it compares the number of observed differences against the expected differences given the quality scores. * Updated the SAM input/output code to use the new standard for encoding annotations via CT and PT fields. Additionally tag directions are now supported by Gap5. * New Shuffle Pads and Remove Pad Columns commands. The latter is a fast and simple function, while Shuffle Pads performs full realignments, much like Gap4. * New function: Disassemble Contigs. This is a fast alternative to Disassemble Readings, but is limited to entire contigs at a time. * New function: Lists -> Contigs to Readings. Turns a list of contig names into a list of sequences within those contigs. * Find Read Pairs now has an option to filter the results by library and by the number of spanning read-pairs between each pair of contigs. * Added Check Assembly function. This compares the used/visible portion of a sequence against the consensus to identify sequences that align badly. (It doesn't yet have the gap4 functionality of aligning the cutoff data too.) * The Restriction Enzyme Plot from gap4 has been added to gap5. This works as per gap4 except for the ability to create tags, which can be added at a later stage if desired. * Added a Check Database function. It's slow, but a useful sanity check for me during development, and maybe for others. There is a CLI version of this called "gap5_check". This function also has an option to fix any data corruptions found. Please make sure you backup your database first before using this feature as it is not guaranteed to be an improvement in all scenarios. * Numerous contig editor updates: - Bulk trimming is now possible using < and > keys within the consensus. - The contig editor now has functions to select and deselect all sequences at a particular consensus column (or overlapping or within a given range). - Added a Group Readings feature. This provides options to vertically reorder the sequences by a variety of primary and secondary collations. - More search modes: "depth <" and "depth >" to look for low and high depth regions; SNP and discrepancy score searches, utilising the new consensus algorithm; search from file (equivalent to the old gapNav interface in Gap4). - The sequence names panel now colours the names according to the consistency/validity of the templates. The colours are: white = ok pair blue = single ended orange = pair, spanning contigs red = inconsistent orientation grey = consistent orientation, but distance too large or too small. This also required a few tweaks to the colouring of the name display and UI controls. The Quality button now only turns quality grey-scales on and off for sequence bases, not the mapping qualities. Instead the Settings menu has two radio buttons to toggle between template status and mapping quality for the names panel. This only has an effect when in Pack Sequences mode; the one sequence per line mode has room to display both pieces of information and so always does so. - Added the Join To command in the names popup menu for read-pairs that span contigs. The Go To menu item has also been updated to report the observed insert size. - Added an option to Break Contig at a specific position. - Implemented a simplistic approach for computing unpadded consensus coordinates. This uses the cached consensus sequence, which can now be updated from within the contig editor too (so it may ask to save changes even when it's simply to add more cached data), so it is far faster than gap4. However it is still linear time based on the number of fragments and consensus length. The editor "goto" box in the bottom left still works on padded or reference coordinates as listed by the P or R button, but manually adding the letter 'u' after a number will request unpadded coord. The P/R button hasn't been made P/R/U yet as the display of coordinates will be too slow still. There are more explicit padded vs unpadded options in the search dialogue, or hitting Return in the editor consensus will also show that coordinate. Other Gap5 Updates ------------------ * More contig editor updates: - Added the ability to copy and paste contig names as well as reading names from the editor window. Also rebound Button-2 to be copy by #number, with Button-1 still being "name". - The contig editor now allows "n" or "-" to be typed in. Also added Insert keybinding as for insertng pads ("i" still works). - We now disallow tags at the ends of contigs in the "cutoff" portion of a contig. Ie where sequence cutoff data resides, but no more non-cutoff bases exist. It is still permitted to have tags within a "hole" inside a contig, just not at the ends. - Increased the default size of the tag editor window. Also disabled the line wrapping, so the horizontal scrollbar should be used for long lines. - Clicking on a base within the tag now displays the summary data of the base underneath it instead of repeating the mouse-over text. This is the same interface as gap4 now. - When invoking the editor by reading name it now brings the editor up on the first visible base of that sequence, instead of the first potentially-clipped base. - The Editor search dialogue window now has Page Up and Page Down keybindings to perform previous and next search (as per Gap4's key bindings). Control-S and Control-R no longer create new windows each time either. - Improved editor search UI. Hovering over the Search button in the dialogue window will now highlight which editor of an join editor pair will be searched in. (As before, left-clicking in an editor will change this, only now it's obvious this happens.) Plus the editor cursor of an inactive editor in a join-editor pair is no longer solid, when visible. Instead it is a hollow square. - Searching by sequence name or #number in the editor now positions the editing cursor on the first used base instead of the first base (whether or not in cutoff data). - The editor Trace Display is now aligned against sequences. This means scrolling and dragging also works. In addition the Lock button has been fixed. - Any case where the editor cursor goes off screen due to using left/right arrow keys or performing a search now scrolls the editor so the last 10 characters are now the first 10 characters, meaning it jumps by almost one screen full. Previously it scrolled such that 10 more characters would appear. - The contig editor width and height and the horizontal position of the name / sequence split pane is now remembered if the Settings -> Save Settings menu item is used. - Added an editor method to shift entire portions of an alignment left/right. (Experimental.) * Increased the word size in Find Repeats and some other optimisations - now dramatically faster, often 100x improvement. Improved FIJ speed some more too. Removing the Contig Selector plots is also now far faster (approx 1500x faster in the extreme case of 1 million repeat hits). * tg_index now has a "-v version" option to request generating older format gap5 databases. * SAM support: - Duplicates are no longer entered by default in tg_index. Use tg_index -D to force these to be entered. - We no longer need headers (eg @SQ) when reading SAM files. - Improved support for "*" in sequence records within SAM. (They get treated as "N" for now, in the absense of any reference.) Also improved error handling for malformed files. - Exporting in SAM format now provides an option to use unpadded reference coordinates rather than the old mode of padded only. This is more alike the pair-wise alignments that are expected from short-read aligners. * Major overhaul of insertion and deletion of pads in the consensus. These used to insert to or delete from every sequence overlapping that point regardless of whether that position was in the sequence cutoff data. Now we only edit sequences that overlap in used non-cutoff data. * The List Contigs window now has a Control-A keybinding. Additionally Copy and Paste should now copy all selected rather than just the first 4Kb or so. * Break Contig now has an option to further split the right-hand contig up if the break caused "holes" to appear. Also added a Remove Contig Holes command to break contigs around sequence holes. * Improved contig number handling: #<record> now works in addition to =<record>; List Contigs report improved. * The Contig ID component of dialogues now uses the visible start/end portion of a contig instead of just going from base 1 to the contig length. This mainly prevents cases of runs of Ns appearing on the ends of consensus when saving just a single contig. * Sequence Search (main menu, outside of the editor) no longer brings up a separate editor every time the Next button is pressed, instead preferring to reuse existing ones if available. It also underlines the matched sequence in the contig editor. * The Template display now has various quality plots. They're turned off by default as they incur a substantial speed penalty. * The number of annotations is now tracked per bin, and hence per contig, as per sequences. Using this we now also have a far faster algorithm for searching through annotations when very few exist. (The needle in haystack problem.) * Code reorganisation: merged the tgap and gap5 directories for reasons of sanity and removal of circular dependencies between the two. * Removed a lot of the debugging output. It can be reenabled by running "gap5 -debug 1". * Improved debugging tools and checking for validity of data via checksums. * Added SVN revision numbers to the version strings reported by most of the main programs. * Improved robustness of databases; crashes while flushing writes should now roll back to the previous state rather than giving a corrupted DB. * Removed error signal handlers in gap4 and gap5 so that crashes are easier to debug on linux. For some reason calling abort from a signal handler often ends up with a stack that gdb will not list. * Renamed Disassemble Contigs to Delete Contigs and rearranged the Edit menu a bit. * Tweaks to the Find Internal Joins algorithm to hopefully find some more small matches. * Added the ability to rename contigs and to change their starting location. Gap5 Bug Fixes -------------- * Numerous Disassemble Readings bug fixes: - Fixed numerous data corruptions: bin placements, contig sizes, tag misplacments, sequence orientation (apparent misaligments). - Improved robustness when facing sequences which no longer exist. - Fixed an issue that could sometimes leave zero-read contigs instead of deleting the contig. - Fixes to the B+Tree sequence name index: now correctly - removing the entry when duplicate names exist, fixed an - issue where we removed whole branches of the tree. - Improved contig hole detection. * Break Contig bug fixes: - Numerous data corruption fixes; bin placements, contig sizes, tag misplacments, tag clipping at contig ends. - Fixed an issue where cached consensus sequences were sometimes counted in the number of sequences within a contig. - Added a check to see if breaking at this position will produce a contig with zero sequences. If so abort early rather than create an inconsistency. - Fixed cache reference counting issues. - Fixed out by one error in determining whether to move data to right contig. - Removed referene counting errors. * Join Contigs bug fixes: - Major bug fix to prevent misaligned joins. If editing cursor is not visible and lock mode is not enabled, the save while joining caused the contigs to shift positions, breaking alignment. - Bringing up the join editor should now set the editing cursor to the correct sequence. - Fixed potential bug in joining contigs causing it to fail to delete the old right hand contig. (We have seen this, but not 100% sure this fixes it.) - When quitting the Join Editor and not making a join, it would only offer to save changes to 1 of the 2 contigs. It now does both. - The differences line in the join editor should no longer find false matches when searching backwards. - Backwards searching for sequence should no longer mission occasional (approx 1 in 1000) matches. - It's no longer possible to attempt a join to itself. (Could be achieved before by using multiple join editor windows up simultaneously.) - The join editor now has the top and bottom contigs correctly ordered, once again agreeing with the title bar ("a / b" meaning contig a on top and contig b on the bottom. - Fixed some editor sizing issues when using non-standard font sizes. This was showing up as the consensus line sometimes being invisible in the Join Editor. - Fixed some reference counting bugs. These typically showed up as assertion failures and crashes. - Create Tag now works on both editors in a Join Editor. * Contig Editor bug fixes: - Fixed a rather common crash & assertion failure (caused by mismatching reference counting on copy-on-write objects). - Fixed redisplay bugs when edits are made in a join editor being updated in another window. - The tags added by the Find Primer-Walk function are now positioned correctly for both strands (reverse was incorrect before). - Fixed a bug that caused empty Tk error dialogues to appear when clicking on locations with no sequence data within the contig editor, but only after attempting to edit a contig with an invalid name. - Fixed a major issue with using Save in the Contig Editor followed by continued editing. The items saved then became "live" and any changes made could end up being automatically written to disk regardless of whether the user did a second save. - Removing tags via the editor was still leaving them in bin hierarchies, causing corruptions in some cases. Fixed. - Fixed a contig editor bug where attempting to remove a column in the contig cutoff regions (before first or after last visible base) would work if the first/last base was "*". - Inserting columns in the consensus now behaves better at extreme places (eg 1st base in far-left cutoff). - Many bug fixes to editor Undo, especially in relation to inserting and removing columns at the first and last bases in sequences or the contig. - The contig editor now correctly responds to notifications that the program is trying to shut down, asking the user if they wish to save. Formly it would sometimes simply crash. Cut and pasting of complemented sequences now works. * Various caching/reference counting bug fixes: - Fixed some caching bugs with the B+Tree code, showing up as crashes or corruptions. - Fixed a memory corruption in the consensus caching code, caused when a bin considerably shrinks. - Removed a few gap5-cache related bugs (assertions, corruptions, crashes). - Fixed issues with complementing of cached consensus sequences. - The consensus cache can no longer return sections of blank N data. This happened when a contig start precisely matched the root bin start point. - Fixed a bug in reference counting in the consensus algorithm, sometimes showing up as crashes in gap5_consensus tool. - Removed several reference count leaks in List Contigs, Save Consensus and consensus iterators. This included things like the consensus computed for Find Internal Joins. - Fixed a problem causing the consensus cache invalidation to sometimes miss invalidating regions. * Contig ID handling: - When using dialogues asking for a single contig and a range within it (eg Save Consensus) it now correctly sets the default start and end positions based on the clipped consensus coordinates, instead of just 1 to contig-length. - It should no longer be possible to duplicate contig names when importing new reads. - Lists containing the same contig multiple times (either explicitly or implicitly by using different read IDs within the same contig) are now filtered out in functions taking lists of contigs (eg Find Internal Joins). * Exporting data: - Fixed a bug in Export Contigs to SAM format involving the handling of template names. It could sometimes cause a crash. - Exporting a portion of a single contig in Export Sequences now correctly outputs all the annotations, even if they're outside the desired range (by attached to readings that are overlapping the range). - Removed extraneous newline that sometimes appears in fasta or fastq outputs. * Importing Data: - Sequences imported via Assembly -> Import... now have their sequence names indexed, meaning we can search for them by name. - Fixed parsing errors with CAF format; quality lines starting with white space are no longer a problem; backslash \ continuation line support added; improved quote handling; support for reading CAF on Windows. - Removed crashes when parsing malformed FASTA files. - Importing from fasta files should be more robust now. - Fixed a stack corruption when importing from ACE. Sequences imported now also have a mapping score of 255. - Fixed a bug in fasta import where the last sequence in a fasta file often generated a blank contig. - Use of binary I/O modes on Windows (BAM). * Template display: - Complemeted contigs in the Template Display sometimes wrongly caused templates to be flagged as inconsistent. Now fixed. - The template display now correctly starts up showing the start of a contig when that contig does not start as base 1. - The depth plot in the template display should more accurately reflect the actual depth at a variety of zoom levels instead of artificially increasing depth as we zoom out. * Various data-editing fixes (mostly solving data corruptions): - When removing a consensus column causes removal of an item from the contig, we now also update the bin and contig extents incase the removal changed them. Similarly inserting columns could sometimes fail to update contig extents. - Deleting consensus bases such that entire tags or sequences are removed now correctly updates no.seq and no.anno fields in the bins. - Added write-lock to bins when removing items. This could cause some data to not be written back to disk if unmodified by another function, or for editor edits to be pushed to main gap5 I/O without hitting Save. (A potentially major corruption) - Fixed bugs in range updates when inserting and removing to sequences. (Minor issue) - Fixed a memory corruption when we remove the last item from a bin. - Adding new sequences to complemented contigs could create incorrect sequencing positionings if the smallest bin had grown, triggering a new leaf node. Also correted some house-keeping coordinates (start/end used) for complemented bins. - Fix for 1bp long sequences and updating the bin ranges. - Moving sequences could sometimes cause them to flip orientation. - Fixed a major corruption involving reuse of bin-range slots. This could cause overwriting of some data once we've managed to remove 2 or more items from a bin and then start to reuse those slots. - Major bug fix to moving contigs in the contig selector - it can no longer duplicate contigs and in the process remove an existing one. - Fixed a bug when writing bins that previously contained data but no longer do. - Added bin simple loop detection in the various functions to increment or decrement the number of seqs, annotations and reference position markers. (This shouldn't happen, but it's a robustness improvement.) * Internal change to storage of annotations. If attached to a sequence they now should always be placed in the same internal contig-bin as their associated sequence. This fixes a number of bugs and simplifies some algorithms. Older databases are not restricted in this manner and so the change is backwards compatible. * Tags are now displayed in strict left to right order rather than the broken right to left order as before. * Removed various bugs with allocating and deallocating tags (caused by misunderstanding my own code and the meaning of the "idx" field). * Removed a memory overrun when running Find Internal Joins or Find Repeats with lots of small contigs. * Complement Contig via the List Contigs window now works. * The program now knows the proper filename of the database when opened using the File -> Open dialogue and browsing to another directory. This was causing errors in Check Database. * Worked around issues with metacity window manager and refusals to raise windows. Ensure that as many dialogues as possible are correctly parented, otherwise metacity can gift focus to a window that isn't even visible. (This is a WM bug.) * Several bug fixes involving detection of empty bins. * Robustness improvements: consensus when faced with corrupted databses and the contig selector when trying to draw zero contigs. * Fixed the consensus when consisting soley of reads of N. * Fixed crashes in Complement Contig in some cases (typically very deep data). * Saved settings in various dialogues now write to .gap5rc instead of .gaprc. * Gap5 now checks the master database version and will no longer automatically start updating individual records to the latest encoding/formats if the database is an older format. This allows testing of newer versions without risking the inability to revert back. * Truncated read system calls now handled in bam reading, instead of interpreting these as EOF. * The lowest level of Gap5 I/O code no longer simply aborts on an error, but now whinges instead and passes the error up one level. (The calling procedure may still abort though.) Gap4 fixes ---------- * Fixed a (rare) infinite loop in the trace display code. * Fix crash in Find Internal Joins when faces with lots of small contigs and insufficient reserved space for the consensus. Misc ---- * Bug fixed the "File does not exist" error dialogue * Various compilation improvements: PPC64 detection for MacOS X; rpath support. * Various minor compilation improvements, removing warnings and fixing compilation issues with gcc 4.4.4 onwards and use of _FORTIFY_SOURCE. * Support added for using Tcl 8.5.
Source: README, updated 2011-12-05