2003-10-29 12:46 Ilya Dondoshansky * blastool.c (6.254), blastutl.c (6.418), mbalign.c (6.41), mblast.c (6.191), mblast.h (6.47): Allow 2-stage greedy extension in megablast 2003-10-30 13:37 Ilya Dondoshansky * blastutl.c (6.419): Fix for megablast with non-greedy traceback 2003-11-05 16:11 Ilya Dondoshansky * mblast.c (6.192): Fix for traceback with greedy algorithm 2003-11-06 14:52 Ilya Dondoshansky * blastdef.h (6.150): Added error MBTemplateType, so it can be returned when wordsize/template length combination is wrong 2003-11-06 14:53 Ilya Dondoshansky * mblast.c (6.193): Fix in MegaBlastSetupSearchInternalByLoc when query submitted as Bioseq instead of SeqLoc; removed unused variables 2003-11-07 16:52 Ilya Dondoshansky * gapxdrop.c (6.76): Fixed SEMI_G_ALIGN_EX so it produces correct scores, by making code exactly correspond to ALIGN_EX 2003-11-10 11:59 Ilya Dondoshansky * blastool.c (6.255): Print the seqid in AcknowledgeBlastQuery for any non-local id 2003-11-10 15:15 Ilya Dondoshansky * blast.c (6.392): Bug fix in BLASTMergeHsps 2003-11-19 13:09 Ilya Dondoshansky * blast.c (6.393): Use consistent rounding in length adjustment calculation 2003-11-24 17:06 Tom Madden * blastutl.c (6.420): Tblastn optimization, only fetch part of sequence needed 2003-11-26 14:08 Tom Madden * blastkar.c (6.91): simplified BlastKarlinLtoH and BlastKarlinLHtoK and provided better protection against overflow, new function NlmKarlinLambdaNR (all from Mike Gertz) 2003-11-26 14:09 Tom Madden * blastkar.h (6.32): Remove ref to BlastKarlinLambdaBis (no longer needed per Mike Gertz) 2003-11-26 14:09 Tom Madden * newkar.c (6.4): impalaKarlinLambdaNR now uses NlmKarlinLambdaNR (from Mike Gertz) 2003-11-28 10:16 Christiam Camacho * blastkar.c (6.92): Combine newkar.c's contents with blastkar.c 2003-11-28 13:34 Christiam Camacho * newkar.c (6.5): Contents moved to blastkar.c 2003-11-28 17:39 Christiam Camacho * blastkar.c (6.93), blastkar.h (6.33): +static keyword to BlastKarlinLtoH 2003-11-29 22:36 Christiam Camacho * blastkar.c (6.94): Fix compilation error 2003-12-01 14:15 Tom Madden * kappa.c (6.35): Add one byte to filteredMatchingSequence to prevent ABR/ABW 2003-12-02 21:10 Jonathan Kans * ncbisrti.h (6.3): added defines missing from Mac OS 10.3 headers 2003-12-10 11:53 Ken Katz * spidey.c (6.65): Ensured that 'ovl' when used is never negative once set in SPI_AdjustOverlaps() [see revision 6.57] 2003-12-10 12:05 Ilya Dondoshansky * blast.c (6.394), blastutl.c (6.421), mblast.c (6.194), mblast.h (6.48): Added function ReevaluateScoreWithAmbiguities to reevaluate score for one HSP; use it after greedy traceback 2003-12-11 18:46 Ilya Dondoshansky * blastutl.c (6.422): Correction in setting hit ranges after repeats filtering 2003-12-12 11:00 Tom Madden * blastkar.c (6.95): Add gap_decay_rate to BlastCutoffs, remove BlastCutoffs_simple, protection against overflow, removal of defunct _real variables (all from Mike Gertz) 2003-12-12 11:00 Tom Madden * blastkar.h (6.34): Add gap_decay_rate to BlastCutoffs, remove BlastCutoffs_simple, removal of defunct _real variables (all from Mike Gertz) 2003-12-12 11:01 Tom Madden * blast.c (6.395), blastool.c (6.256): Change to signature of BlastCutoffs, remove BlastCutoffs_simple 2003-12-12 12:57 Ken Katz * spidey.c (6.66): Fixed a potential array bounds read error in SPI_CheckMrnaOrder() 2003-12-12 16:25 Ken Katz * spidey.c (6.67): Fixed bug in SPI_CheckForPolyAExon() where multiple SeqAlignPtr's to the same object were not handled carefully: one of the ptr's was being accessed when the object was freed via the other ptr. 2003-12-23 18:28 Ilya Dondoshansky * blastool.c (6.257): Use number of identities from the seqalign to calculate percent identity in tabular output 2003-12-29 10:42 George Coulouris * blast.c (6.396), blastconcat.c (1.5), blastconcatdef.h (1.2): tblastn query concatenation fixes from morgulis 2003-12-29 10:51 George Coulouris * blastdef.h (6.151): Bump version, use __DATE__ instead of hardcoded date 2003-12-29 16:45 George Coulouris * salign.c (6.7): Remove unnecessary comparison 2003-12-30 10:14 Christiam Camacho * blastool.c (6.258): Fix to MergeDbGiListsWithOIDLists: When searching gi lists for matches in rdfp linked list, isolate each element of the linked list first. 2004-01-02 08:44 George Coulouris * blastdef.h (6.152): Revert to hardcoded BLAST_RELEASE_DATE 2004-01-02 13:11 Jonathan Kans * actutils.c (6.35): Sqn_GlobalAlign2Seq flips code break, anticodon when reverse complementing sequence 2004-01-05 17:09 Tom Madden * blastdef.h (6.153): Put back dashes in date 2004-01-06 12:48 Ilya Dondoshansky * kappa.c (6.36): Do not free Karlin block in RedoAlignmentCore, because its pointer is passed outside 2004-01-06 17:36 Ilya Dondoshansky * blastpri.h (6.110): Added BLAST_HSPFree function that frees the edit block and the HSP 2004-01-06 17:37 Ilya Dondoshansky * blast.c (6.397), mblast.c (6.195): Use BLAST_HSPfree function 2004-01-06 17:37 Ilya Dondoshansky * blastutl.c (6.423): Use BLAST_HSPfree function; in particular fixes a bug with wrong memory being freed 2004-01-09 13:13 Ilya Dondoshansky * blastutl.c (6.424): In [Get,Check]StartForGappedAlignment: if posMatrix not available, use square matrix for calculations 2004-01-12 18:06 Christiam Camacho * readdb.c (6.425): Sort link bit gi lists 2004-01-13 10:46 Ilya Dondoshansky * mblast.c (6.196): Changed cast to nearest integer in length adjustment calculation 2004-01-14 12:01 Ilya Dondoshansky * blastutl.c (6.425): Gapped alignment is position based only if posMatrix exists 2004-01-16 18:43 Ilya Dondoshansky * blastpri.h (6.111), blastutl.c (6.426), mblast.h (6.49), mblast.c (6.197): No more need for special argument for partial search: it is set in options 2004-01-23 16:13 Christiam Camacho * readdb.c (6.426): 1. Refactored code to create multiple volumes. 2. Set the maximum sequence file size to 1GB. 2004-01-23 17:29 Ilya Dondoshansky * mblast.c (6.198): Increase hitlist size for preliminary alignment if traceback is delayed 2004-01-25 00:06 Ilya Dondoshansky * blastutl.c (6.427): Translate only relevant parts of long subject sequences for tblastn traceback 2004-01-26 08:52 Christiam Camacho * readdb.c (6.427): Do not use snprintf 2003-10-29 12:48 Ilya Dondoshansky * megablast.c (6.108): Added -D4 option for 2-stage greedy gapped extension with format identical to -D2 2003-10-30 12:30 Ilya Dondoshansky * megablast.c (6.109): Fixed error in previous commit - output file pointer has to be set for all cases 2003-10-31 16:43 Ilya Dondoshansky * blast_driver.c (1.10): Use gapped_calculation boolean from score options 2003-10-31 16:56 Ilya Dondoshansky * blast_driver.c (1.11): Correction for setting genetic code string in options 2003-11-04 18:17 Ilya Dondoshansky * blast_driver.c (1.12): Set PHI BLAST options when pattern is specified 2003-11-05 17:28 Ilya Dondoshansky * blastall.c (6.136), megablast.c (6.110): No need to shift subsequence coordinates in tabular output, since they are already shifted in the seqalign 2003-11-12 13:22 Ilya Dondoshansky * blast_driver.c (1.13): Change greedy option from boolean to integer, as in C++ application; some minor memory leak fixes 2003-11-14 13:07 Jonathan Kans * rtestval.c (1.11): set alignFindRemoteBsp, doSeqHistAssembly if validateAlignments 2003-11-20 10:44 Christiam Camacho * copymat.c (6.26): Tom Madden's changes to use lookup table contruction code from algo/blast. 2003-11-21 13:01 Vladimir Ivanov * copymat.c (6.27): Added extern definition for impalaMakeFileNames() 2003-11-24 13:18 George Coulouris * copymat.c (6.28): Correction to previous fix for 64-bit irix 2003-12-01 09:51 Jonathan Kans * tbl2asn.c (6.72): added environmental sequence to list of recognized organisms 2003-12-02 10:39 Jonathan Kans * tbl2asn.c (6.73): set vsp->seqSubmitParent flag to suppress no pub validator warning 2003-12-03 11:26 Christiam Camacho * blast_driver.c (1.14): Fixes to allow building blast application 2003-12-03 12:35 Ilya Dondoshansky * blast_driver.c (1.15): Renamed BlastMask to BlastMaskLoc, BlastResults to BlastHSPResults 2003-12-09 11:28 Jonathan Kans * tbl2asn.c (6.74): added Aspergillus nidulans FGSC A4 2003-12-10 15:46 Jonathan Kans * tbl2asn.c (6.75): leave unrecognized bracketed information in title 2003-12-23 16:14 Jonathan Kans * tbl2asn.c (6.76): raised to version 2.7 2004-01-02 13:46 George Coulouris * debruijn.c (1.1): Application to generate de Bruijn sequences 2004-01-02 17:13 George Coulouris * debruijn.c (1.2): Add rcsid, correctly handle GetArgs() return value 2004-01-05 15:44 George Coulouris * debruijn.c (1.3): Fix fencepost error, improve argument handling 2004-01-07 09:40 Jason Papadopoulos * blast_driver.c (1.16): initialize all fields of readdb struct 2004-01-12 14:47 Jonathan Kans * tbl2asn.c (6.77): decline to instantiate protein titles if feature indexes were dropped, raised version number 2004-01-26 14:40 George Coulouris * copymat.c (6.29): * Correct buffer overrun * Use offset rather than pointer in LookupBackboneCell 2004-01-27 15:47 Ilya Dondoshansky * megablast.c (6.111): Set no_traceback option to 2 for -D4, 1 for -D0, 0 for others 2004-01-28 12:40 Jonathan Kans * tbl2asn.c (6.78): added ReplaceOneRNA - processing of .rna file somehow disappeared from source code in cvs 2004-01-28 13:22 Jonathan Kans * tbl2asn.c (6.79): do not set RNA editing exception if different, require entry in feature table 2004-01-29 09:56 Christiam Camacho * formatdb.c (6.92): Removed -A option, FORMATDB_VER_TEXT no longer supported