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Time	Activity Type	By
2010-May-25
15:13:29	Commit: Removing seqdoc.macosx.powerpc because seqdoc.c source changed since this binary's creation and I no longer have access to a PowerPC machine to compile a new binary.	Jonathan Magasin
15:10:22	Commit: Updated GForge path to seqdoc_plus project. Also cosmetic changes: reformatted to use all 80 columns.	Jonathan Magasin
2010-May-07
03:35:35	Commit: Removing copyright info from original SeqDoC Perl script because incorrect to have in seqdoc.c, a reimplementation (with some modifications) of the SeqDoC algorithm.	Jonathan Magasin
2010-Apr-28
17:53:05	Commit: Updated native Windows seqdoc binary.	Jonathan Magasin
00:11:52	Commit: Updating README to reflect new binaries: no PowerPC any more. Note that the native Windows binary still needs to be updated, and hopefully can find a PowerPC machine to update/reinclude that binary. To be done this week.	Jonathan Magasin
00:08:49	Commit: Installing new binaries for the latest src/seqdoc.c. These all produce absolutely identical difference traces for the TestData. Note that I am not yet including an updated native Windows binary, just the Cygwin binary today. Also not including the Po...	Jonathan Magasin
00:05:03	Commit: Minor changes in expected output due to seqdoc.c fix. Earlier version sometimes output at peaks a neighboring peak's quality value (pretty sure).	Jonathan Magasin
00:01:31	Commit: Minor fprintf() change to avoid (recent in GCC) compiler warning.	Jonathan Magasin
2010-Apr-27
15:08:47	Commit: Check if nothing on STDIN (user forgot to < input file) and if so give usage info.	Jonathan Magasin
01:13:34	Commit: Bug fix to check_local_difference() so that it correctly looks for the closest test peak. Bad index for for loop:( This fixes '?' annotation and greatly reduces '#' output, which is now more accurate.	Jonathan Magasin
2009-Dec-19
20:52:51	Commit: Adding University of California copyright and Educational Community License v2.0 info to source and README.txt.	Jonathan Magasin
2009-Nov-16
16:23:39	Commit: First version of SeqDoc+ tools. Software is as submitted with manuscript to BioMed Central except for some minor updates to seqdoc.c and to the copyright/licensing text in all source.	Jonathan Magasin
16:14:58	Commit: First install of SeqDoC+ source, binaries, and sample/test data.	Jonathan Magasin

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Description
SeqDoC+ consists of: seqdoc, a utility based on Mark Crowe's SeqDoC for comparing a pair of Sanger-sequencing DNA traces to identify point mutations; and additional scripts for identifying discrepancies between the raw DNA trace comparison and a BLAST alignment of the corresponding inferred sequences. Positions in the BLAST alignment that are unsupported by SeqDoC may suggest point mutations or base caller errors that would go undetected if one relied solely on the inferred DNA sequences.
Developer Info
Jonathan Magasin
Trove Categorization
Development Status: 1 - Planning Intended Audience: Other Audience License: GNU General Public License (GPL) Operating System: Linux, MacOS, Microsoft, Windows Programming Language: C, Perl Spoken Language: English Topic: Bio-Informatics

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SeqDoC+