What's new in Staden Package 2.0.0 Beta 9
Dec 16, 2011
- 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.
New in Staden Package 2.0.0 Beta 8 (Feb 9, 2011)
- Microsoft Windows version. The code should now compile and run
- under MinGW/Msys on windows.
- MacOS X updates: improved compilation and fixed a few Mac
- specific display glitches.
- Various code tidyups - less compiler warnings, more portable
- for linux variants (eg Centos).
- Removed dependency on samtools. (This also avoids a few
- samtools related bugs, but hopefully not creating new ones to
- replace them.)
- Removed dependency on IncrTcl, IncrTk, IncrWidgets. These can
- still be used for one part of Gap4 (prefinish GUI) but the
- code will build and execute without these now.
New in Staden Package 2.0.0 Beta 7 (Jul 15, 2010)
- Gap5 changes:
- Added an Import GFF Annotations option to Gap5. This deals
- with padded and unpadded data, although for now the GFF types
- are not used, instead using the "type=;" attribute
- in the last GFF column to select a gap5 tag type. GFF Export
- has been improved too.
- Tg_index now has support for spliced alignments in SAM/BAM,
- using the CIGAR "N" character. This isn't fully implemented
- yet as the read-pairing breaks in this case, but the data at
- least can be imported now.
- Gap5 should now compile under MacOS X, provided the X11
- version of Tcl/Tk is used rather than native aqua.
- Extra contig-editor search methods - by annotation, by tag
- type.
- Selecting large regions is easier in the contig editor now. It
- either auto-scrolls at the window edge or we can use
- shift+click to extend.
- Gap5 now has basic primer-walking oligo picking support. (PCR
- to come later.)
- Improvements to SAM support: fixed flags when exporting; tags
- are supported (via user-defined key=value auxillary data - Zs
- and Zc record types) in both import/export; faster export;
- output is now sorted; protection against quality values higher
- than ASCII ~; now parse the PL field in read-group lines in
- tg_index.
- The Join Editor now displays overlap length and match score,
- confirming whether we still wish to make a join. Also
- bug-fixed the align button when one or both contigs didn't
- start at base position 1.
- Two new scripts: gap5_consensus, gap5_export. These wrap up
- gap5 menu items as non-interactive command line tools.
- The contig editor has a Goto... menu to jump to other
- sequences on this template.
- It should be easier to keep track of sequences when scrolling
- in the editor as it attempts to adjust the Y scrollbar to keep
- data on screen. Additionally the Y-layout doesn't change so
- much when scrolling rightwards (although left scrolling still
- changes Y layout). Improved efficiency by caching some more
- data.
- The contig editor now sorts by sequence technology first and
- then X coordinate, meaning that ABI capillary sequences are
- always at the top of the display. NOTE: This requires the
- platform tag (PL) in SAM/BAM @RG read-group header lines.
- Bug fix writing reading names when importing a mixture of data
- with and without read-groups.
- Fixed the Map Reads interface, when adding to contigs that do
- not start at base 1. Also fixed some memory free issues here.
- The Show Diagonal and Clear All commands of the contig
- selector window now work. The results menu (and Results
- Manager window) now update too.
- Disable a few more options and buttons when in read-only
- mode. Previously it wouldn't actually have written data, but
- tried and aborted.
- Fixed a rare bug with single base-pair tags vanishing under
- certainc onditions.
- Other changes:
- [Gap4/Gap5] Updated the primer melting temperature code to use
- the latest published formulae.
- Various compilation improvements: better detection of Large
- File Support under some linux systems; control over the
- location of curses/ncurses libraries (and which to use); fixed
- "make depend" when running from a subdirectory instead of the
- top src root; forced use of the staden os.h instead of
- sometimes picking up a copy in io_lib.
New in Staden Package 2.0.0 Beta 6 (Mar 29, 2010)
- Fixed an error causing crashes when decoding sequence names of varying lengths coming from multiple read-groups.