What's New in PipTools (mostly-C version)
- 2003-Nov-4
-
- Bug fix: use of reserved function names starting with "is" was
tripping up some compilers.
- Minor updates in the installation documentation re: Boulder.
- 2002-Jan-24
-
- Strong-hits has new "-gap" and "-step" options that allow nearby
segments to be combined for meeting the length requirement.
- Bug fix: strong-hits now rejects the "-inseq2" and "-exons-only"
options when no interval file is specified.
- The SUFF2 setting for DOS/Windows in the sample Makefile now
installs the three Perl programs with an empty file extension, so
you don't have to type ".pl" to run them.
- Various updates, corrections, additions, and clarifications in the
documentation, especially the installation pages.
- 2001-Oct-23
-
- A bug has been fixed in the program PipMaker uses to compute the
"concise textual form of the alignments". It was failing to convert
the second-sequence endpoints of reverse-complement alignments into
the user's original coordinates. This in turn affected output from
the PipTools that use these concise files (strong-hits, transform-pos,
and where-hit). Lav files ("raw blastz output") did not have this
problem. Note that the PipTools are unchanged, and output
from PipMaker should be correct now.
- 2001-Sep-18
-
- Bug fix: strong-hits was computing segment lengths 1 nt too short.
- Strong-hits has a new "-exons-only" option that instructs it to
ignore the intervals for genes and translated regions when looking
for overlaps in an exons file.
- 2001-Aug-14
- Programs
- Bug fix: exons2mrna did not read arguments correctly on some systems.
- Minor bug fixes and/or improvements in genscan2exons, strong-hits,
transform-pos, sort-exons, find-cpg, and parsing of interval files.
- Better compatibility with older compilers.
- Makefile now runs piplib/Makefile correctly, and is more Windows-friendly.
- Perl source files are named with ".pl" to avoid confusion.
- Documentation
- Sample installation walk-through for Win98.
- Minor additions and clarifications in other documents.
- 2001-Jul-5
-
- The find-cpg program is now case-insensitive.
- 2001-Jun-27
-
- In the labeled underlay format (produced by genscan2underlays
and exons2underlays via the -laj option), the "dummy"
item is no longer needed.
- Misc. minor improvements to the documentation.
$Revision: 1.7 $$Date: 2003/11/04 22:18:05 $