1995.1 Changes and Bug Fixes

1. Pregap
   • The "eba" phase was always running eba on the first reading in the input list.
   • Correctly handles cases where the ID/EN lines are named differently from the experiment file filename.
   • Support for odd reading names, such as those that exist but are blank, or that contain spaces.
   • Better ALF support (reading name generation).
   • Interactive clipping using the trev program (a new version of ted).
   • Uses the vepe screen against vector instead of the gap option.

2. Gap
   • More robust with inputting invalid CS line input or zero length files
   • Bug fixes with X11 timings during contig editor quit align command in contig editor works better
   • Removed memory leak from enter preassembled data. Also no longer crashes then the input file of filenames does not exist. More robust when we have no LN/LT/SQ lines.
   • Fixed file permissions after copy database
   • Busy files renamed to PROJECT.V.BUSY
   • Tags of precisely length 1 previously sometimes caused problems
   • Fixed buffer overrun in save consensus tags (which caused blank output files under SunOS 4). We also support specifying ranges for this now
   • Removed cross hair usage for "find read pairs" (it didn't work)
   • Corrected assembly alignment failure error code (was 5, now 2). Also some readings were failing incorrectly when requesting not to join.
   • Break contig is more intelligent in cases where breaking at a single reading would generate more than 2 contigs.
   • Disassembly previously could corrupt the tag lists.
   • Removed ABMG tag from the standard GTAGDB file.

3. Vepe
   • Added "screen for restriction sites"
   • Added "screen against vector"
   • Cosmid vector search now locates the left and right ends.

4. Trace file IO (within gap, gap4, ted, makeSCF, etc)
   • Programs using SCF files now support the older SCF format too.
   • ABI reading code will now recognise the simplest forms of MacBinary and automatically strip off the header (this assumes it's 128 bytes).
   • Added getABIstring and getABIcomment functions to the ABI io library.
   • Updated getABISampleName. As before, but greatly simplified code.
   • New getABIdate command.
   • Better support for reading experiment files via the trace level interface. We have better support for writing back to the original experiment file.

5. A new trace viewer program, named trev, to replace ted.
   • Improved user interface.
   • Better integration with experiment files.

6. Gcgentryname2
   • New version of gcgentryname2 to support their new format.

7. Clip
   • No longer crashes when run on blank files.

8. Convert
   • Program is more reliable when converted from bap to gap.
   • The default quality value for bases has been changed from 0 to 100.