CVS log for RATools/ra

CVS log for RATools/ra_gridalign.c
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Revision 1.16 / (view) - annotate - [select for diffs] , Wed Apr 19 22:20:14 2006 UTC (5 years, 9 months ago) by kristian
Branch: MAIN
CVS Tags: HEAD
Changes since 1.15: +5 -2 lines
Diff to previous 1.15

Added conformance threshold [0,1]. This is specifically designed for chips that
may not be fully covered with target DNA.

Updated run_all.pl to incorporate the conformance threshold.

Revision 1.15 / (view) - annotate - [select for diffs] , Wed Apr 19 21:08:05 2006 UTC (5 years, 9 months ago) by kristian
Branch: MAIN
Changes since 1.14: +7 -13 lines
Diff to previous 1.14

Fixed bugs in gridalignment

Revision 1.14 / (view) - annotate - [select for diffs] , Tue Jan 31 12:45:48 2006 UTC (6 years ago) by dcutler
Branch: MAIN
Changes since 1.13: +1 -1 lines
Diff to previous 1.13

Nimblegen flipped their definition of forward and reverse strand.  Gridalignment
adapted.

Revision 1.13 / (view) - annotate - [select for diffs] , Thu Jan 12 19:02:58 2006 UTC (6 years ago) by dcutler
Branch: MAIN
Changes since 1.12: +28 -18 lines
Diff to previous 1.12

Other fixes for Nimblegen chips

Revision 1.12 / (view) - annotate - [select for diffs] , Thu Jan 12 18:45:20 2006 UTC (6 years ago) by dcutler
Branch: MAIN
Changes since 1.11: +1 -0 lines
Diff to previous 1.11

Nimblegen as started making one of the fields in their NDF file optional.
Hacked gridalignment to deal with this.

Revision 1.11 / (view) - annotate - [select for diffs] , Mon May 16 21:03:25 2005 UTC (6 years, 8 months ago) by dcutler
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10

Restoring the higher threshold to consider a chip properly aligned

Revision 1.10 / (view) - annotate - [select for diffs] , Mon May 16 20:54:43 2005 UTC (6 years, 8 months ago) by dcutler
Branch: MAIN
Changes since 1.9: +69 -47 lines
Diff to previous 1.9

More attempts to save poor to mediocre chips

Revision 1.9 / (view) - annotate - [select for diffs] , Wed May 4 11:21:17 2005 UTC (6 years, 9 months ago) by dcutler
Branch: MAIN
Changes since 1.8: +27 -27 lines
Diff to previous 1.8

Fixed defaulting back to the best alignment, when the chip is very poor
in all alignments.

Revision 1.8 / (view) - annotate - [select for diffs] , Thu Apr 28 19:44:23 2005 UTC (6 years, 9 months ago) by dcutler
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7

Increased the stringency before quitting trying to  align the grid

Revision 1.7 / (view) - annotate - [select for diffs] , Wed Apr 27 20:17:44 2005 UTC (6 years, 9 months ago) by dcutler
Branch: MAIN
Changes since 1.6: +8 -7 lines
Diff to previous 1.6

Minor bug fixes

Revision 1.6 / (view) - annotate - [select for diffs] , Fri Feb 11 16:46:26 2005 UTC (6 years, 11 months ago) by dcutler
Branch: MAIN
CVS Tags: rel-1-0-5
Changes since 1.5: +2 -1 lines
Diff to previous 1.5

Minor bug fixes

Revision 1.5 / (view) - annotate - [select for diffs] , Tue Feb 8 18:23:38 2005 UTC (6 years, 11 months ago) by dcutler
Branch: MAIN
Changes since 1.4: +118 -28 lines
Diff to previous 1.4

Lot's of bug fixes and additions.   Principle among them

1) Now uses estimate of the corners of the chip from the Affy scanner
software

2) Works on most (all??) genotyping chips, including 100k and forth coming
500k

3) Implemented a "global" estimate of feature variance to help stablize
parameter choice for resequencing on smaller feature chips.

4) Loads of minor crashing bugs fixed in grid alignment.

Revision 1.4 / (view) - annotate - [select for diffs] , Thu Aug 19 16:58:18 2004 UTC (7 years, 5 months ago) by dcutler
Branch: MAIN
CVS Tags: rel-1-0-3
Changes since 1.3: +1 -0 lines
Diff to previous 1.3

Update to use Nimblegen Arrays natively

Revision 1.3 / (view) - annotate - [select for diffs] , Thu Aug 19 16:55:04 2004 UTC (7 years, 5 months ago) by dcutler
Branch: MAIN
Changes since 1.2: +183 -48 lines
Diff to previous 1.2

Update to use Nimblegen Arrays natively

Revision 1.2 / (view) - annotate - [select for diffs] , Sat Aug 7 16:48:19 2004 UTC (7 years, 6 months ago) by dcutler
Branch: MAIN
Changes since 1.1: +176 -55 lines
Diff to previous 1.1

Major Update to Deal with Genotyping Chips

Revision 1.1.1.1 / (view) - annotate - [select for diffs] (vendor branch) , Mon Jul 26 22:49:08 2004 UTC (7 years, 6 months ago) by opendpgp
Branch: opendpgp
CVS Tags: start, rel-1-0-2, rel-1-0-1
Changes since 1.1: +0 -0 lines
Diff to previous 1.1

Initial Import

Revision 1.1 / (view) - annotate - [select for diffs] , Mon Jul 26 22:49:08 2004 UTC (7 years, 6 months ago) by opendpgp
Branch: MAIN

Initial revision

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Contact: kristian_stevens@sbcglobal.net

CVS log for RATools/ra_gridalign.c

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