2007-10-08 15:53 talioto * geneid/: param/human.070606.u2branch.ppt.param (1.1), src/RequestMemory.c (1.17): Added human parameter file with U2 branch point and poly-Py tract. Bug-fix: corrected initialization of nExons. 2007-08-07 19:01 talioto * geneid/: include/geneid.h (1.41), src/BuildAcceptors.c (1.7), src/BuildDonors.c (1.5), src/BuildU12Acceptors.c (1.5), src/manager.c (1.13): Fixed off by one error in BuildDonors and Build(U12)Acceptors to predict splice sites at end of sequence correctly 2007-08-01 15:45 talioto * geneid/: include/geneid.h (1.40), param/human3isoU12.param (1.3), src/CookingGenes.c (1.27), src/PrintExons.c (1.19), src/Translate.c (1.12): Translation/evidence bug fix 2007-07-05 17:21 talioto * geneid/include/geneid.h (1.39): changed Rsites to 4 to accommodate gc donors 2007-07-05 16:39 talioto * geneid/include/geneid.h (1.38): changed Rsites to 3 to accommodate gc donors 2007-07-05 16:33 talioto * geneid/: include/geneid.h (1.37), src/ScoreExons.c (1.17): changed LENGTHSi back to 100000 2007-06-22 15:58 talioto * geneid/src/Translate.c (1.11): Fixed bug in translation of evidence Introns. 2007-06-06 12:26 talioto * geneid/: include/geneid.h (1.36), src/BuildAcceptors.c (1.6): Lengthened locus name length to 500. Removed U2 branch point contribution to score. 2007-04-25 19:20 talioto * geneid/: Makefile (1.13), include/geneid.h (1.35), src/RequestMemory.c (1.16), src/ScoreExons.c (1.16), src/SortExons.c (1.15), src/genamic.c (1.17), src/manager.c (1.12): Updated Makefile and header file 2007-04-25 11:08 talioto * geneid/: Makefile (1.12), include/geneid.h (1.34), src/CookingGenes.c (1.26), src/Translate.c (1.10), src/genamic.c (1.16): Fixed bug in Translate 2007-04-04 14:40 talioto * geneid/: include/geneid.h (1.33), src/CookingGenes.c (1.25), src/PrintExons.c (1.18): Evidence introns can now be printed 2007-04-04 13:11 talioto * geneid/src/SortSites.c (1.1): Added module to sort sites 2007-04-04 13:10 talioto * geneid/src/BuildZeroLengthExons.c (1.1): Adding support for RSS sites 2007-04-04 12:25 talioto * geneid/: include/geneid.h (1.32), src/BuildAcceptors.c (1.5), src/BuildU12Acceptors.c (1.4), src/readparam.c (1.14): BP and PPT distances and related parameters added to profile heading in parameter file. 2007-04-03 14:39 talioto * geneid/src/: CookingGenes.c (1.24), Translate.c (1.9), genamic.c (1.15): Fixed printing of genes with evidence introns 2007-04-02 17:50 talioto * geneid/src/: PrintExons.c (1.17), genamic.c (1.14): Bug fix: coordinates fixed for intron evidence given with -R option 2007-03-30 17:09 talioto * geneid/: Makefile (1.11), include/geneid.h (1.31), param/human3isoU12.param (1.2), src/CookingGenes.c (1.23), src/Output.c (1.18), src/PrintExons.c (1.16), src/ReadExonsGFF.c (1.10), src/RequestMemory.c (1.15), src/SortExons.c (1.14), src/SwitchFrames.c (1.7), src/genamic.c (1.13), src/geneid.c (1.24), src/readargv.c (1.21): prerelease 3: geneid combiner 2007-01-23 15:48 talioto * geneid/: include/geneid.h (1.30), src/genamic.c (1.12), src/geneid.c (1.23), src/readparam.c (1.13): RSS don and acc cutoffs specified in paramfile 2007-01-11 18:52 talioto * geneid/: Makefile (1.10), include/geneid.h (1.29), param/human.061209.param (1.2), src/BuildInternalExons.c (1.10), src/CookingGenes.c (1.22), src/Output.c (1.17), src/PrintExons.c (1.15), src/RequestMemory.c (1.14), src/ScoreExons.c (1.15), src/SortExons.c (1.13), src/SwitchPositions.c (1.6), src/genamic.c (1.11), src/manager.c (1.11): Updated RSS prediction feature and Evidence Introns feature 2006-12-21 15:03 talioto * geneid/src/geneid.c (1.22): [no log message] 2006-12-21 14:56 talioto * geneid/: include/geneid.h (1.28), src/BuildInitialExons.c (1.9), src/BuildInternalExons.c (1.9), src/CookingGenes.c (1.21), src/PrintExons.c (1.14), src/ScoreExons.c (1.14), src/genamic.c (1.10), src/geneid.c (1.21), src/manager.c (1.10), src/readargv.c (1.20), src/readparam.c (1.12): v1.3 Public Preview Release 1 2006-12-18 13:02 talioto * geneid/: Makefile (1.9), include/geneid.h (1.27), src/BackupGenes.c (1.8), src/BuildDonors.c (1.4), src/CookingGenes.c (1.20), src/CorrectExon.c (1.6), src/PrintExons.c (1.13), src/SwitchFrames.c (1.6), src/genamic.c (1.9), src/geneid.c (1.20), src/manager.c (1.9), src/readparam.c (1.11): Geneid v1.3 PR3 2006-12-13 12:28 talioto * geneid/: Makefile (1.8), include/geneid.h (1.26), src/BackupGenes.c (1.7), src/DumpHash.c (1.8), src/GetSitesWithProfile.c (1.9), src/GetStopCodons.c (1.9), src/RequestMemory.c (1.13), src/SortExons.c (1.12), src/SwitchFrames.c (1.5), src/genamic.c (1.8), src/geneid.c (1.19), src/manager.c (1.8): Version 1.3 PR2 2006-12-11 10:57 talioto * geneid/param/human.061209.param (1.1): [no log message] 2006-12-11 10:50 talioto * geneid/: src/BackupGenes.c (1.6), src/BuildAcceptors.c (1.4), src/BuildDonors.c (1.3), src/BuildInitialExons.c (1.8), src/BuildInternalExons.c (1.8), src/BuildORFs.c (1.4), src/BuildSingles.c (1.5), src/BuildSort.c (1.4), src/BuildTerminalExons.c (1.7), src/BuildU12Acceptors.c (1.3), src/ComputeStopInfo.c (1.3), src/CookingGenes.c (1.19), src/CorrectExon.c (1.5), src/Dictionary.c (1.7), src/DumpHash.c (1.7), src/FetchSequence.c (1.4), src/GetSitesWithProfile.c (1.8), src/GetStopCodons.c (1.8), src/Output.c (1.16), src/PrintExons.c (1.12), src/PrintSites.c (1.10), src/ReadExonsGFF.c (1.9), src/ReadGeneModel.c (1.7), src/ReadHSP.c (1.4), src/ReadSequence.c (1.7), src/RecomputePositions.c (1.5), src/RequestMemory.c (1.12), src/ScoreExons.c (1.13), src/SearchEvidenceExons.c (1.8), src/SetRatios.c (1.4), src/SortExons.c (1.11), src/SortHSPs.c (1.2), src/SwitchFrames.c (1.4), src/SwitchPositions.c (1.5), src/Translate.c (1.8), src/account.c (1.6), src/beggar.c (1.5), src/genamic.c (1.7), src/geneid.c (1.18), src/manager.c (1.7), src/readargv.c (1.19), src/readparam.c (1.10), include/geneid.h (1.25): Geneid pre 1.3 release 2006-11-03 15:22 talioto * geneid/src/BuildAcceptors.c (1.3): Fixed branch point context calculation for U2 branch points. 2006-10-25 11:59 talioto * geneid/src/PrintExons.c (1.11): Updated to make GFF3 compliant 2006-10-25 11:50 talioto * geneid/src/PrintExons.c (1.10): Updated to make GFF3 compliant 2006-06-02 11:53 talioto * geneid/src/readargv.c (1.18): minor fix to usage statement 2006-06-01 23:06 talioto * geneid/src/SortExons.c (1.10): Added lowerlimit and upperlimit args to properly insert ghost exons. 2006-06-01 23:05 talioto * geneid/src/geneid.c (1.17): Added lowerlimit argument to Output call and lowerlimit and upperlimit args to SortExons call. 2006-06-01 23:02 talioto * geneid/src/PrintSites.c (1.9): Added lowerlimit argument to handle overlaps properly. 2006-06-01 22:59 talioto * geneid/src/Output.c (1.15): Added lowerlimit argument. 2006-06-01 22:58 talioto * geneid/include/geneid.h (1.24): Updated prototypes for Output, PrintSites with lowerlimit argument. 2006-05-29 17:53 talioto * geneid/src/geneid.c (1.16): Fixed bugs. 2006-05-29 16:03 talioto * geneid/include/geneid.h (1.23): Added RU12EXONS and RU12SITES. Changed other values (MAXGENE, MAXNSEQUENCES, MAXSTRING) back to previous geneid v1.2 values. 2006-05-29 16:00 talioto * geneid/src/readargv.c (1.17): Added U12 option (-U) which must be used along with U12 parameter file. 2006-05-29 15:59 talioto * geneid/src/RequestMemory.c (1.11): Now uses U12-specific max sites and exons. 2006-05-29 15:58 talioto * geneid/src/SetRatios.c (1.3): Now calculates U12-specific max sites and exons using RU12SITES and RU12EXONS. 2006-05-29 15:56 talioto * geneid/src/BuildU12Acceptors.c (1.2): Now uses the MAX number of U12 sites. 2006-05-29 15:55 talioto * geneid/src/BuildDonors.c (1.2): Now takes the MAX number of sites as last argument. 2006-05-29 15:53 talioto * geneid/src/: BuildInitialExons.c (1.7), BuildInternalExons.c (1.7), BuildTerminalExons.c (1.6): Now takes the MAX number of exons as last argument. 2006-05-29 15:52 talioto * geneid/src/readparam.c (1.9): Made string comparison case insensitive to be more tolerant of varied capitalization of headers. Also made backward compatible with mis-spelled param file headers, e.g. 'weigths'. 2006-05-29 15:49 talioto * geneid/src/beggar.c (1.4): Corrected memory calculation. 2006-05-29 15:47 talioto * geneid/src/manager.c (1.6): Max number of U12 splice sites and flanking exons passed to Site and Exon builder functions. 2006-05-29 15:46 talioto * geneid/src/geneid.c (1.15): Memory only allocated for U12 splice sites and flanking exons if needed. 2006-05-26 18:12 talioto * geneid/src/RequestMemory.c (1.10): Rolled back last change. 2006-05-26 15:33 talioto * geneid/src/RequestMemory.c (1.9): U12 modification. Only request memory for U12 strucures (sites and exons) if needed. 2006-05-26 15:29 talioto * geneid/src/beggar.c (1.3): U12 modification. Corrected calculation of MemSites. 2006-05-26 15:28 talioto * geneid/include/geneid.h (1.22): Reduced size of string for the site subtype to decrease memory footprint. 2006-05-26 01:39 talioto * geneid/include/geneid.h (1.21): Changed VERSION back to 1.2. We will modify the version number in the future when we decide to make an official tarball release 2006-05-26 01:36 talioto * geneid/src/readargv.c (1.16): Made usage statement clearer. 2006-05-26 01:07 talioto * geneid/src/geneid.c (1.14): Bug fix. Calculation of lower and upper bounds fixed to avoid out of bounds error. 2006-05-26 00:58 talioto * geneid/src/CookingGenes.c (1.18): Bug fix. Fixed error in printing of amino acid length in gene comments. 2006-05-25 19:36 talioto * geneid/src/CookingGenes.c (1.17): Fixed cDNA printing bug. 2006-05-25 17:47 talioto * geneid/param/human3isoU12.param (1.1): GeneID parameter file with U12 intron support 2006-05-25 17:41 talioto * geneid/Makefile (1.7): Added BuildU12Acceptors and BuildDonors modules. 2006-05-25 17:39 talioto * geneid/include/geneid.h (1.20): U12 modifications and new print functions. 2006-05-25 17:16 talioto * geneid/src/readparam.c (1.8): Added optional reading of U12 parameters and profiles. 2006-05-25 17:04 talioto * geneid/src/readargv.c (1.15): Added optional protein sequence printing (PSEQ - option A). Added GFF3 printing (GFF3 - option 3). Added lower and upper bounds for prediction on sequence (LOW - option j, HI - option k). Added intron printing (INTRON - option n). 2006-05-25 16:59 talioto * geneid/src/manager.c (1.5): U12 modification. Added U12 Exon building. GetSitesWithProfile is now only used for Start codons. Support for specification of lower and upper bound coordinates to restrict the sequence on which gene prediction is run. 2006-05-25 16:51 talioto * geneid/src/geneid.c (1.13): U12 modification. U12 flags initialized. Additional options added: GFF3 output, printing of amino acid sequence, and specification of lower and upper bound coordinates to restrict the sequence on which gene prediction is run. 2006-05-25 16:46 talioto * geneid/src/genamic.c (1.6): U12 modification. Donor and acceptor subtypes must match and U12 thresholds (exon score and splice site score sums) must be met in order to be compatible. 2006-05-25 16:44 talioto * geneid/src/CookingGenes.c (1.16): Removed output of GFF3 FASTA directive when no sequences to print. 2006-05-25 16:43 talioto * geneid/src/Output.c (1.14): Fixed error in format of GFF3 seq_region directive. 2006-05-25 16:35 talioto * geneid/src/account.c (1.5): U12 modification. Added accounting of U12 sites and exons. 2006-05-25 16:32 talioto * geneid/src/: SortExons.c (1.9), SwitchPositions.c (1.4): U12 modification. Support for U12 Exon Types. 2006-05-25 16:31 talioto * geneid/src/ScoreExons.c (1.12): U12 modification. Support for U12 Exon Types. U12 exon weight supplied in param file is applied. 2006-05-25 16:27 talioto * geneid/src/RequestMemory.c (1.8): U12 modification. Support for U12 splice sites, exons and profiles. 2006-05-25 16:23 talioto * geneid/src/RecomputePositions.c (1.4): U12 modification. Support for U12 splice sites. 2006-05-25 16:20 talioto * geneid/src/PrintSites.c (1.8): U12 modification. Added output subtype as well as BP and PPT positions. 2006-05-25 16:18 talioto * geneid/src/PrintExons.c (1.9): U12 modification. Added output of gene, mRNA and intron gff records. Support for GFF3 output. 2006-05-25 16:15 talioto * geneid/src/Output.c (1.13): U12 modification. Support for output of U12 sites and exons. Support for GFF3 output. 2006-05-25 16:10 talioto * geneid/src/GetSitesWithProfile.c (1.7): U12/U2 modification. Support for additional U2 subtypes like GC-AG. 2006-05-25 16:08 talioto * geneid/src/CorrectExon.c (1.4): U12 modification. Support for additional U12 Exon Types. 2006-05-25 16:07 talioto * geneid/src/CookingGenes.c (1.15): U12 modification. Support for additional U12 Exon Types. Support for GFF3 output. Support for printing of introns in GFF format. Printing of amino acid sequence was made optional. 2006-05-25 16:03 talioto * geneid/src/BuildU12Acceptors.c (1.1): U12 modification. New module for building U12 acceptor sites. Based on BuildAcceptors.c. 2006-05-25 15:59 talioto * geneid/src/: BuildInitialExons.c (1.6), BuildInternalExons.c (1.6), BuildTerminalExons.c (1.5): U12 modification. ExonType not hardcoded. 2006-05-25 15:55 talioto * geneid/src/BuildDonors.c (1.1): The BuildDonors.c module was not properly added to the cvs repository. No updates were made to this module since the geneid_v1.2 release. 2006-05-25 15:50 talioto * geneid/src/BuildAcceptors.c (1.2): Searching of PPT and branch point profiles modified 2006-05-25 15:45 talioto * geneid/src/BackupGenes.c (1.5): Site subtype and PPT and branch point scores and locations are now backed up 2004-09-16 15:32 eblanco * geneid/include/geneid.h (1.19, geneid_v1_2): Setting a different config. of memory: MAXHSPs MAXSEQUENCES 2004-09-16 15:32 eblanco * geneid/src/ScoreExons.c (1.11, geneid_v1_2): Fixing bug 2004-04-30 18:10 eblanco * geneid/src/ScoreExons.c (1.10): Fixing the bug in the compatibility blast-geneid frames 2004-04-23 18:22 eblanco * geneid/docs/chapter2/index.html (1.4, geneid_v1_2): adding comment about X's 2004-04-23 18:12 eblanco * geneid/src/ReadHSP.c (1.3, geneid_v1_2): removing the requirement about sorting HSPs before input to geneid 2004-04-22 16:15 eblanco * geneid/docs/images/SR.jpg (1.3, geneid_v1_2): new image 2004-04-22 16:11 eblanco * geneid/docs/chapter9/code_html/BuildAcceptors.html (1.1, geneid_v1_2): adding the source code explanation 2004-04-22 16:10 eblanco * geneid/docs/chapter9/index.html (1.4, geneid_v1_2): adding BuildAcceptors 2004-04-22 15:59 eblanco * geneid/docs/chapter9/code_html/beggar.html (1.1, geneid_v1_2): memory required for current sequence processing 2004-04-22 15:58 eblanco * geneid/docs/chapter9/code_html/SortHSPs.html (1.1, geneid_v1_2): HSP quick-sort doc 2004-04-22 15:51 eblanco * geneid/include/geneid.h (1.18): updating defines for MAXHSP and MAXNSEQUENCES 2004-04-22 15:50 eblanco * geneid/Makefile (1.6, geneid_v1_2): updating gcc path 2004-04-22 15:29 eblanco * geneid/Makefile (1.5): updating gcc 2004-04-22 15:23 eblanco * geneid/include/geneid.h (1.17): increasing MAXNSEQUENCES -> 1000 2004-04-22 15:14 eblanco * geneid/docs/chapter10/index.html (1.4, geneid_v1_2): updating releasing year to 2004 2004-04-22 15:12 eblanco * geneid/docs/chapter8/index.html (1.5, geneid_v1_2): creating branch point and ppts section 2004-04-22 14:52 eblanco * geneid/docs/chapter2/index.html (1.3): adding Poly Pyrimidine Tract and BPoints 2004-04-22 14:46 eblanco * geneid/include/geneid.h (1.16): Adding the ACCEPTOR_CONTEXT to look for branch points 2004-02-12 18:09 eblanco * geneid/Makefile (1.4): [no log message] 2004-02-03 11:24 eblanco * geneid/: src/CookingGenes.c (1.14, geneid_v1_2), src/ScoreExons.c (1.9), include/geneid.h (1.15): [no log message] 2004-02-03 11:18 eblanco * geneid/src/Dictionary.c (1.6, geneid_v1_2): 'X' substituted for UNKNOWNAA (geneid.h) 2004-02-03 10:54 eblanco * geneid/src/SortExons.c (1.8, geneid_v1_2): GENE_SCORE TO 0.0 (0, before) 2004-01-27 17:29 eblanco * geneid/include/geneid.h (1.14): adding new attributes to support the prediction of combined acceptor, branchpoints and pptracts 2004-01-27 17:27 eblanco * geneid/src/readargv.c (1.14, geneid_v1_2): rewriting help menu messages (force genes) 2004-01-27 17:25 eblanco * geneid/src/SortExons.c (1.7): insert first and last artificial exons in the prediction 2004-01-27 17:23 eblanco * geneid/src/ScoreExons.c (1.8): fixing some bugs in the HSP system 2004-01-27 17:23 eblanco * geneid/src/ReadGeneModel.c (1.6, geneid_v1_2): forcing the creation of ghost exons to start and end the prediction 2004-01-27 17:22 eblanco * geneid/src/geneid.c (1.12, geneid_v1_2): update calls to HSP routines 2004-01-27 17:20 eblanco * geneid/src/SortHSPs.c (1.1, geneid_v1_2): quicksort of input HSPs 2004-01-27 17:19 eblanco * geneid/src/RequestMemory.c (1.7, geneid_v1_2): Request memory for new structures related to acceptor sites 2004-01-27 17:18 eblanco * geneid/src/readparam.c (1.7, geneid_v1_2): reading branch point & pptracts before acceptor splite profile 2004-01-27 17:16 eblanco * geneid/src/ReadHSP.c (1.2): Reading HSPs (no order is required) 2004-01-27 17:15 eblanco * geneid/src/PrintSites.c (1.7, geneid_v1_2): Printing different acceptor site features 2004-01-27 17:13 eblanco * geneid/src/BuildAcceptors.c (1.1, geneid_v1_2): Detection of acceptors using: - acceptor AG core - PPTract - Branch point 2004-01-15 11:47 eblanco * geneid/src/manager.c (1.4, geneid_v1_2): Changing GetSitesWithProfile for Acc for BuildAcceptors (using 3 profiles) 2004-01-14 10:44 eblanco * geneid/docs/chapter9/index.html (1.3): adding SortHSPs.c 2004-01-14 10:29 eblanco * geneid/docs/chapter9/code_html/ReadHSP.html (1.2, geneid_v1_2): It is not needed that HSPs are ordered 2004-01-14 10:26 eblanco * geneid/docs/chapter7/index.html (1.5, geneid_v1_2): The requirement of HSPs sorted is not needed 2003-12-04 16:37 eblanco * geneid/param/: human3iso.param (1.3), plasmodium.param (1.2), tetraodon.param (1.2), wheat.param (1.2) (utags: geneid_v1_2): Adding rules for starting/ending predictions... 2003-12-04 16:33 eblanco * geneid/param/: dros.param (1.3), dictyostelium.param (1.2), human1iso.param (1.3) (utags: geneid_v1_2): Adding rules for starting/ending predictions... 2003-12-03 17:54 eblanco * geneid/docs/chapter8/index.html (1.4): adding a comment about Begin/End tags in the Gene Model 2003-11-13 16:07 eblanco * geneid/src/ReadGeneModel.c (1.5): adding single+ and single- when forcing single-gene per sequence prediction 2003-11-05 16:23 eblanco * geneid/src/ReadSR.c (1.5): update geneid 1.2 2003-11-05 16:14 eblanco * geneid/README (1.2, geneid_v1_2): update geneid 1.2 2003-11-05 16:09 eblanco * geneid/src/: SortExons.c (1.6), SwitchFrames.c (1.3, geneid_v1_2), SwitchPositions.c (1.3, geneid_v1_2), Translate.c (1.7, geneid_v1_2): update geneid 1.2 2003-11-05 16:05 eblanco * geneid/src/: SearchEvidenceExons.c (1.7), SetRatios.c (1.2) (utags: geneid_v1_2): update geneid 1.2 2003-11-05 16:02 eblanco * geneid/src/: RequestMemory.c (1.6), ScoreExons.c (1.7): update geneid 1.2 2003-11-05 15:58 eblanco * geneid/src/RecomputePositions.c (1.3, geneid_v1_2): update geneid 1.2 2003-11-05 15:54 eblanco * geneid/src/: readparam.c (1.6), ReadSequence.c (1.6, geneid_v1_2): update geneid 1.2 2003-11-05 15:50 eblanco * geneid/src/: ReadGeneModel.c (1.4), ReadHSP.c (1.1): update geneid 1.2 2003-11-05 15:46 eblanco * geneid/src/: readargv.c (1.13), ReadExonsGFF.c (1.8, geneid_v1_2): update geneid 1.2 2003-11-05 15:43 eblanco * geneid/src/: CookingGenes.c (1.13), GetSitesWithProfile.c (1.6, geneid_v1_2), GetStopCodons.c (1.7, geneid_v1_2), PrintSites.c (1.6): update geneid 1.2 2003-11-05 15:40 eblanco * geneid/src/: manager.c (1.3), Output.c (1.12, geneid_v1_2), PrintExons.c (1.8, geneid_v1_2): update geneid 1.2 2003-11-05 15:36 eblanco * geneid/src/: geneid.c (1.11), GetSitesWithProfile.c (1.5), GetStopCodons.c (1.6): update geneid 1.2 2003-11-05 15:23 eblanco * geneid/src/: FetchSequence.c (1.3), genamic.c (1.5) (utags: geneid_v1_2): update geneid 1.2 2003-11-05 15:20 eblanco * geneid/src/: CookingGenes.c (1.12), CorrectExon.c (1.3, geneid_v1_2), Dictionary.c (1.5), DumpHash.c (1.6, geneid_v1_2): update geneid 1.2 2003-11-05 15:14 eblanco * geneid/docs/: chapter4/sequence/5seqs.fa (1.1, geneid_v1_2), chapter4/sequence/tmp.evi (1.1, geneid_v1_2), chapter4/sequence/tmp.hsp (1.1, geneid_v1_2), images/SR.jpg (1.2): update geneid 1.2 2003-11-05 15:10 eblanco * geneid/param/: dictyostelium.param (1.1), dros.param (1.2), human1iso.param (1.2), human3iso.param (1.2), plasmodium.param (1.1), tetraodon.param (1.1), wheat.param (1.1): update geneid 1.2 2003-11-05 14:39 eblanco * geneid/src/: BuildTerminalExons.c (1.4), ComputeStopInfo.c (1.2) (utags: geneid_v1_2): update geneid 1.2 2003-11-05 14:36 eblanco * geneid/src/BuildSort.c (1.3, geneid_v1_2): update geneid 1.2 2003-11-05 14:32 eblanco * geneid/src/: BuildInternalExons.c (1.5), BuildORFs.c (1.3), BuildSingles.c (1.4) (utags: geneid_v1_2): update geneid 1.2 2003-11-05 14:27 eblanco * geneid/src/BuildInitialExons.c (1.5, geneid_v1_2): update geneid 1.2 2003-11-05 14:23 eblanco * geneid/src/: BackupGenes.c (1.4), beggar.c (1.2) (utags: geneid_v1_2): update geneid 1.2 2003-11-05 12:55 eblanco * geneid/src/account.c (1.4, geneid_v1_2): update geneid 1.2 2003-11-05 12:48 eblanco * geneid/: include/geneid.h (1.13), Makefile (1.3): update geneid 1.2 2003-11-05 12:13 eblanco * geneid/docs/chapter10/: index.html (1.2), index.html (1.3): update geneid 1.2 2003-11-05 12:07 eblanco * geneid/docs/chapter9/: code_html/geneid.h.html (1.2, geneid_v1_2), index.html (1.2): update geneid 1.2 2003-11-05 11:11 eblanco * geneid/docs/chapter9/code_html/SortExons.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-05 11:04 eblanco * geneid/docs/chapter9/code_html/SearchEvidenceExons.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-05 11:00 eblanco * geneid/docs/chapter9/code_html/ScoreExons.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 18:17 eblanco * geneid/docs/chapter9/code_html/: RequestMemory.html (1.2, geneid_v1_2), ReadHSP.html (1.1): update geneid 1.2 2003-11-04 18:13 eblanco * geneid/docs/chapter9/code_html/ReadExonsGFF.html (1.3, geneid_v1_2): update geneid 1.2 2003-11-04 18:00 eblanco * geneid/docs/chapter9/code_html/ReadGeneModel.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 17:56 eblanco * geneid/docs/chapter9/code_html/ReadExonsGFF.html (1.2): update geneid 1.2 2003-11-04 17:50 eblanco * geneid/docs/chapter9/code_html/readargv.html (1.3, geneid_v1_2): update geneid 1.2 2003-11-04 16:43 eblanco * geneid/docs/chapter9/code_html/: manager.html (1.2, geneid_v1_2), readargv.html (1.2): update geneid 1.2 2003-11-04 16:39 eblanco * geneid/docs/chapter9/code_html/geneid.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 16:35 eblanco * geneid/docs/chapter9/code_html/BuildInternalExons.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 16:33 eblanco * geneid/docs/chapter9/code_html/BuildInitialExons.html (1.2, geneid_v1_2): [no log message] 2003-11-04 16:13 eblanco * geneid/docs/chapter8/index.html (1.3): update geneid 1.2 2003-11-04 16:02 eblanco * geneid/docs/chapter8/index.html (1.2): update geneid 1.2 2003-11-04 15:44 eblanco * geneid/docs/chapter7/index.html (1.4): update geneid 1.2 2003-11-04 15:39 eblanco * geneid/docs/chapter7/index.html (1.3): update geneid 1.2 2003-11-04 15:36 eblanco * geneid/docs/: chapter7/index.html (1.2), index.html (1.3, geneid_v1_2): update geneid 1.2 2003-11-04 15:28 eblanco * geneid/docs/chapter6/index.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 15:22 eblanco * geneid/docs/: chapter4/index.html (1.2), chapter5/index.html (1.2) (utags: geneid_v1_2): update geneid 1.2 2003-11-04 15:10 eblanco * geneid/docs/chapter4/samples_html/sr.html (1.3, geneid_v1_2): update geneid 1.2 2003-11-04 15:07 eblanco * geneid/docs/chapter4/samples_html/: sr.html (1.2), genes.html (1.3, geneid_v1_2): update geneid 1.2 2003-11-04 15:04 eblanco * geneid/docs/chapter4/samples_html/evidences.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 15:01 eblanco * geneid/docs/chapter4/samples_html/genes.html (1.2): update geneid 1.2 2003-11-04 14:56 eblanco * geneid/docs/chapter4/samples_html/exons.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 14:52 eblanco * geneid/docs/chapter4/formats_html/: gff.html (1.3), xml.html (1.3) (utags: geneid_v1_2): update geneid 1.2 2003-11-04 14:49 eblanco * geneid/docs/chapter4/: samples_html/acceptors.html (1.2, geneid_v1_2), formats_html/geneid.html (1.3), formats_html/geneid.html (1.4, geneid_v1_2): update geneid 1.2 2003-11-04 14:45 eblanco * geneid/docs/chapter4/formats_html/gff.html (1.2): update geneid v 1.2 2003-11-04 14:45 eblanco * geneid/docs/chapter4/formats_html/: xml.html (1.2), extended.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 14:20 eblanco * geneid/docs/chapter4/formats_html/geneid.html (1.2): update geneid 1.2 2003-11-04 12:50 eblanco * geneid/docs/chapter3/index.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 12:46 eblanco * geneid/samples/example3.promoter.gff (1.2, geneid_v1_2): update geneid v 1.2 2003-11-04 12:42 eblanco * geneid/docs/chapter2/index.html (1.2): update geneid v 1.2 2003-11-04 12:41 eblanco * geneid/docs/chapter1/index.html (1.2, geneid_v1_2): update geneid 1.2 2003-11-04 12:37 eblanco * geneid/docs/index.html (1.2): update geneid v 1.2 2003-09-15 11:55 gparra * geneid/Makefile (1.2): The creation of the ./objects and ./bin directories is now included in the make file. 2003-02-26 14:26 eblanco * geneid/src/ScoreExons.c (1.6): [no log message] 2003-02-26 12:03 eblanco * geneid/src/PrintSites.c (1.5): adding default brancches in the Switches in PrintSite 2003-02-26 11:59 eblanco * geneid/src/DumpHash.c (1.5): adding ......exon = NULL; in getExonDumpHash 2003-02-26 11:58 eblanco * geneid/src/Dictionary.c (1.4): key and aa set to zero in GetKey and GetAA 2003-02-26 11:56 eblanco * geneid/src/CookingGenes.c (1.11): adding ..... tmpDNA = NULL; 2003-02-26 11:55 eblanco * geneid/src/BuildInternalExons.c (1.4): LowestLocalExon to 0 2003-02-26 11:50 eblanco * geneid/src/BuildInitialExons.c (1.4): Setting LowestLocalExon to 0 the first time 2003-02-26 11:48 eblanco * geneid/src/geneid.c (1.10): three pointers to NULL when they are not used (compiler warnings) 2003-02-26 11:43 eblanco * geneid/src/manager.c (1.2): adding the value to this counter: allExons->nORFs = 0; if not selected (option Z) 2003-02-26 11:39 eblanco * geneid/src/GetStopCodons.c (1.5): increasing the dimension of the array dono (+1) 2002-04-16 18:05 eblanco * geneid/src/CookingGenes.c (1.10): Setting the LOCUS_gene key in both the predicted protein and cDNA 2002-04-11 16:51 eblanco * geneid/src/PrintExons.c (1.7): Changing the format for exons belonging to genes: LOCUSNAME_number of gene 2002-04-11 16:34 eblanco * geneid/src/ReadSR.c (1.4): Fixing an error about MAXEVIDENCES instead of MAXSR 2002-03-20 12:26 gparra * geneid/docs/: chapter4/formats_html/extended.html (1.1), chapter4/formats_html/geneid.html (1.1), chapter4/formats_html/gff.html (1.1), chapter4/formats_html/xml.html (1.1), chapter4/samples_html/acceptors.html (1.1), chapter4/samples_html/evidences.html (1.1), chapter4/samples_html/exons.html (1.1), chapter4/samples_html/genes.html (1.1), chapter4/samples_html/sr.html (1.1), chapter4/sequence/test.fa (1.1, geneid_v1_2), chapter9/code_html/BackupGenes.html (1.1, geneid_v1_2), chapter9/code_html/BuildInitialExons.html (1.1), chapter9/code_html/BuildInternalExons.html (1.1), chapter9/code_html/BuildORFs.html (1.1, geneid_v1_2), chapter9/code_html/BuildSingles.html (1.1, geneid_v1_2), chapter9/code_html/BuildSort.html (1.1, geneid_v1_2), chapter9/code_html/BuildTerminalExons.html (1.1, geneid_v1_2), chapter9/code_html/ComputeStopInfo.html (1.1, geneid_v1_2), chapter9/code_html/CookingGenes.html (1.1, geneid_v1_2), chapter9/code_html/CorrectExon.html (1.1, geneid_v1_2), chapter9/code_html/Dictionary.html (1.1, geneid_v1_2), chapter9/code_html/DumpHash.html (1.1, geneid_v1_2), chapter9/code_html/FetchSequence.html (1.1, geneid_v1_2), chapter9/code_html/GetSitesWithProfile.html (1.1, geneid_v1_2), chapter9/code_html/GetStopCodons.html (1.1, geneid_v1_2), chapter9/code_html/Output.html (1.1, geneid_v1_2), chapter9/code_html/PrintExons.html (1.1, geneid_v1_2), chapter9/code_html/PrintSites.html (1.1, geneid_v1_2), chapter9/code_html/ReadExonsGFF.html (1.1), chapter9/code_html/ReadGeneModel.html (1.1), chapter9/code_html/ReadSR.html (1.1, geneid_v1_2), chapter9/code_html/ReadSequence.html (1.1, geneid_v1_2), chapter9/code_html/RecomputePositions.html (1.1, geneid_v1_2), chapter9/code_html/RequestMemory.html (1.1), chapter9/code_html/ScoreExons.html (1.1), chapter9/code_html/SearchEvidenceExons.html (1.1), chapter9/code_html/SetRatios.html (1.1, geneid_v1_2), chapter9/code_html/SortExons.html (1.1), chapter9/code_html/SwitchFrames.html (1.1, geneid_v1_2), chapter9/code_html/SwitchPositions.html (1.1, geneid_v1_2), chapter9/code_html/Translate.html (1.1, geneid_v1_2), chapter9/code_html/account.html (1.1, geneid_v1_2), chapter9/code_html/genamic.html (1.1, geneid_v1_2), chapter9/code_html/geneid.h.html (1.1), chapter9/code_html/geneid.html (1.1), chapter9/code_html/manager.html (1.1), chapter9/code_html/readargv.html (1.1), chapter9/code_html/readparam.html (1.1, geneid_v1_2), chapter9/images/V_orange.gif (1.1, geneid_v1_2), chapter9/images/V_silver.gif (1.1, geneid_v1_2) (utags: v1_1_alpha-2002_03_20): added newfiles 2002-03-20 12:20 gparra * geneid/: GNU_PL (1.1, geneid_v1_2), Makefile (1.1), README (1.1), docs/index.html (1.1), docs/chapter1/index.html (1.1), docs/chapter10/index.html (1.1), docs/chapter2/index.html (1.1), docs/chapter3/index.html (1.1), docs/chapter4/index.html (1.1), docs/chapter5/index.html (1.1), docs/chapter6/index.html (1.1), docs/chapter7/index.html (1.1), docs/chapter8/index.html (1.1), docs/chapter9/index.html (1.1), docs/images/SR.jpg (1.1), docs/images/geneid.jpg (1.1, geneid_v1_2), param/dros.param (1.1), param/human1iso.param (1.1), param/human3iso.param (1.1), samples/example1.fa (1.1, geneid_v1_2), samples/example2.evidences.gff (1.1, geneid_v1_2), samples/example2.fa (1.1, geneid_v1_2), samples/example3.EST1.gff (1.1, geneid_v1_2), samples/example3.EST2.gff (1.1, geneid_v1_2), samples/example3.EST3.gff (1.1, geneid_v1_2), samples/example3.fa (1.1, geneid_v1_2), samples/example3.promoter.gff (1.1) (utags: v1_1_alpha-2002_03_20): added newfiles 2002-03-20 11:44 eblanco * geneid/src/: SearchEvidenceExons.c (1.6), SortExons.c (1.5) (utags: v1_1_alpha-2002_03_20): Forcing ci to get rcs files for cvs repository... 2002-03-20 11:32 eblanco * geneid/src/SetRatios.c (1.1, v1_1_alpha-2002_03_20): Initial revision 2002-03-20 11:18 eblanco * geneid/include/geneid.h (1.12, v1_1_alpha-2002_03_20): FINAL VERSION geneid.h for cvs 2002-02-22 14:48 eblanco * geneid/src/readargv.c (1.12, v1_1_alpha-2002_03_20): Display error when unknown option is selected 2002-02-22 14:41 eblanco * geneid/src/readargv.c (1.11): Improving the manual 2002-02-20 18:22 eblanco * geneid/src/RequestMemory.c (1.5, v1_1_alpha-2002_03_20): Adding a factor for the D-array calloc called FDARRAY 2002-02-13 08:26 eblanco * geneid/src/GetStopCodons.c (1.4, v1_1_alpha-2002_03_20): Changing (msg_err) NUMSITES for RSITES 2002-02-13 08:25 eblanco * geneid/src/GetSitesWithProfile.c (1.4, v1_1_alpha-2002_03_20): Changing (err_msg): NUMSITES for RSITES 2002-02-04 10:13 eblanco * geneid/src/Output.c (1.11, v1_1_alpha-2002_03_20): ## to # sequence (space) 2002-02-04 10:12 eblanco * geneid/src/Output.c (1.10): Changing from ## sequence... to # sequence ... 2002-01-29 10:48 eblanco * geneid/src/CookingGenes.c (1.9, v1_1_alpha-2002_03_20): Adding PROMOTER feature to print (if needed, extending elements other than F,I,T and S is easy) 2002-01-18 14:41 eblanco * geneid/src/Dictionary.c (1.3, v1_1_alpha-2002_03_20): "?" changed by "X" (AA) 2002-01-16 09:11 eblanco * geneid/include/geneid.h (1.11): Increasing BASEVALUES_*_LARGE to 100 000 and 50 000 2001-12-18 18:20 eblanco * geneid/include/geneid.h (1.10): geneid v.1.1. final version: parameters set up for chromosome size 2001-12-18 17:28 eblanco * geneid/src/geneid.c (1.9, v1_1_alpha-2002_03_20): geneid v.1.1. final version: * Routines about G+C measurements are placed at ScoreExons * management of calls to predict exons and signals were moved to manager.c * Setratios goes to SetRatios.c * Output GFF exons and genes are directly read as GFF inputs (evidences) 2001-12-18 17:25 eblanco * geneid/src/readparam.c (1.5, v1_1_alpha-2002_03_20): geneid v.1.1. final version: signal profiles are allowed to contain N's whose transitions are computed while reading params 2001-12-18 17:23 eblanco * geneid/src/readargv.c (1.10): geneid v.1.1. final version: XML, cDNA, beggar to show memory amount and more new options supported 2001-12-18 17:22 eblanco * geneid/src/genamic.c (1.4, v1_1_alpha-2002_03_20): geneid v.1.1. final version: stop codons between 2 exons are not allowed to exist 2001-12-18 17:19 eblanco * geneid/src/: beggar.c (1.1), manager.c (1.1) (utags: v1_1_alpha-2002_03_20): Initial revision 2001-12-18 17:18 eblanco * geneid/src/account.c (1.3, v1_1_alpha-2002_03_20): geneid v.1.1. final version 2001-12-18 17:17 eblanco * geneid/src/Translate.c (1.6, v1_1_alpha-2002_03_20): geneid v.1.1. final version: cDNA extraction added 2001-12-18 17:14 eblanco * geneid/src/SwitchPositions.c (1.2, v1_1_alpha-2002_03_20): geneid v.1.1. final version 2001-12-18 17:09 eblanco * geneid/src/SwitchFrames.c (1.2, v1_1_alpha-2002_03_20): geneid v.1.1. final version 2001-12-18 17:05 eblanco * geneid/src/ScoreExons.c (1.5, v1_1_alpha-2002_03_20): geneid v.1.1. final score: * score SR is added after Markov score/filter * there is a min length to use Markov penta/hexanucleotides 2001-12-18 17:00 eblanco * geneid/src/: RecomputePositions.c (1.2, v1_1_alpha-2002_03_20), RequestMemory.c (1.4): geneid v.1.1. final version 2001-12-18 16:56 eblanco * geneid/src/: ReadGeneModel.c (1.3), ReadSR.c (1.3), ReadSequence.c (1.5) (utags: v1_1_alpha-2002_03_20): geneid v.1.1. final version 2001-12-18 16:54 eblanco * geneid/src/ReadExonsGFF.c (1.7, v1_1_alpha-2002_03_20): geneid v.1.1. final version: exon group can be one string 2001-12-18 16:47 eblanco * geneid/src/PrintSites.c (1.4, v1_1_alpha-2002_03_20): geneid version 1.1. final version: includes printing partial signals (filled with "*"'s) 2001-12-18 16:41 eblanco * geneid/src/PrintExons.c (1.6, v1_1_alpha-2002_03_20): geneid v.1.1. final version: OUTPUT genes support XML format 2001-12-18 16:39 eblanco * geneid/src/Output.c (1.9): geneid v.1.1. final version: XML format is supported (OUTPUT) 2001-12-18 16:38 eblanco * geneid/src/GetStopCodons.c (1.3): geneid v.1.1. final version: partial signals and signals containing N's are detected 2001-12-18 16:37 eblanco * geneid/src/GetSitesWithProfile.c (1.3): geneid v.1.1. final version: partial signals are detected as well as signals containing N's 2001-12-18 16:34 eblanco * geneid/src/: DumpHash.c (1.4), FetchSequence.c (1.2) (utags: v1_1_alpha-2002_03_20): geneid v.1.1. final version 2001-12-18 16:29 eblanco * geneid/src/: CorrectExon.c (1.2, v1_1_alpha-2002_03_20), Dictionary.c (1.2): geneid v.1.1. final version 2001-12-18 16:27 eblanco * geneid/src/CookingGenes.c (1.8): geneid v.1.1. final version: includes XML output, cDNA and other features 2001-12-18 16:25 eblanco * geneid/src/ComputeStopInfo.c (1.1, v1_1_alpha-2002_03_20): Initial revision 2001-12-18 16:23 eblanco * geneid/src/BuildTerminalExons.c (1.3, v1_1_alpha-2002_03_20): geneid v.1.1. final version: INPUT sequence to avoid stops between 2 assembled exons 2001-12-18 16:18 eblanco * geneid/src/BuildSort.c (1.2, v1_1_alpha-2002_03_20): geneid v1.1. final version 2001-12-18 16:07 eblanco * geneid/src/BuildSingles.c (1.3, v1_1_alpha-2002_03_20): geneid v.1.1. final version 2001-12-18 16:05 eblanco * geneid/src/BuildORFs.c (1.2, v1_1_alpha-2002_03_20): geneid v1.1. final version 2001-12-18 16:03 eblanco * geneid/src/BuildInternalExons.c (1.3, v1_1_alpha-2002_03_20): geneid v1.1. final version: Input the DNA sequence to check there will not build STOPS among exons 2001-12-18 16:02 eblanco * geneid/src/BuildInitialExons.c (1.3, v1_1_alpha-2002_03_20): geneid v1.1. final version: INPUT the sequence to avoid building STOP codons between 2 exons 2001-12-18 15:57 eblanco * geneid/src/BackupGenes.c (1.3, v1_1_alpha-2002_03_20): geneid 1.1. Final version 2001-10-01 16:44 eblanco * geneid/src/geneid.c (1.8): [no log message] 2001-07-05 09:53 eblanco * geneid/src/readargv.c (1.9): fixing vocabulary 2001-06-25 17:48 eblanco * geneid/src/ReadGeneModel.c (1.2): Adding the reserved word "Infinity" to turn off the DMAX requirement in a GM rule 2001-06-25 15:56 eblanco * geneid/include/geneid.h (1.9): Adding several defines: cDNA string infinity for DMAX isoContext Memory parameters for chromosome-size and normal-size inputs 2001-04-30 16:49 eblanco * geneid/src/Translate.c (1.5): Set free rs var 2001-04-30 15:03 eblanco * geneid/src/Translate.c (1.4): tAA is now a double pointer instead of being an array 2001-04-30 15:02 eblanco * geneid/src/CookingGenes.c (1.7): Vars tAA and info have been changed into pointers instead of being static arrays. 2001-04-25 14:49 eblanco * geneid/src/ReadSequence.c (1.4): Fixing readsequence 2001-04-25 10:29 eblanco * geneid/src/ReadSequence.c (1.3): problems with \r instead of \n 2001-04-25 10:28 eblanco * geneid/src/geneid.c (1.7): Testing bugs (\r) 2001-04-25 10:04 eblanco * geneid/src/readparam.c (1.4): testing possible bugs 2001-04-23 15:56 eblanco * geneid/src/readargv.c (1.8): adding incompatibility option (DG) 2001-04-23 15:12 eblanco * geneid/src/CookingGenes.c (1.6): Adding the capability of writing cDNA from predicted genes 2001-04-23 15:11 eblanco * geneid/src/Translate.c (1.3): Fixing GetcDNA working 2001-04-23 10:58 eblanco * geneid/src/readargv.c (1.7): fixing compilation errors 2001-04-23 10:49 eblanco * geneid/src/readargv.c (1.6): adding cDNA record in the XML DTD 2001-04-23 10:46 eblanco * geneid/src/geneid.c (1.6): adding cDNA falg 2001-04-23 10:45 eblanco * geneid/src/readargv.c (1.5): adding cDNA flag 2001-03-08 16:42 eblanco * geneid/src/Output.c (1.8): Fixing the beginning of XML header 2001-03-08 16:34 eblanco * geneid/src/CookingGenes.c (1.5): Fixing XML bugs 2001-03-08 16:33 eblanco * geneid/src/readargv.c (1.4): fixing XML DTD bugs 2001-03-08 16:18 eblanco * geneid/src/readargv.c (1.3): Adding incompatibility among printing and XML options 2001-03-08 00:00 eblanco * geneid/src/Output.c (1.7): Adding this tag: 2001-03-07 23:55 eblanco * geneid/src/CookingGenes.c (1.4): Adding XML features 2001-03-07 22:07 eblanco * geneid/src/Output.c (1.6): fixing compilation error 2001-03-07 22:05 eblanco * geneid/src/readargv.c (1.2): adding XML options 2001-03-07 21:57 eblanco * geneid/src/Output.c (1.5): Adding XML routines 2001-03-07 21:44 eblanco * geneid/src/geneid.c (1.5): Adding XML flag. 2001-02-14 17:58 eblanco * geneid/src/Translate.c (1.2): Correction for evidence's translation 2001-02-14 17:45 eblanco * geneid/src/PrintExons.c (1.5): Not displaying AA info in GFF format 2001-02-14 17:00 eblanco * geneid/src/geneid.c (1.4): more info on skipping evidences 2001-02-14 16:47 eblanco * geneid/src/ReadExonsGFF.c (1.6): /* Updating sites to the range 0..LengthSequence-1 */ 2001-02-14 16:46 eblanco * geneid/src/PrintExons.c (1.4): Adding conditionals for evidence printing 2001-02-14 16:41 eblanco * geneid/src/SortExons.c (1.4): Fixing the evidences sorting (shifting -COFFSET) 2001-02-14 16:40 eblanco * geneid/src/SearchEvidenceExons.c (1.5): Definitely, right version of the conditional. 2001-02-14 15:52 eblanco * geneid/src/PrintExons.c (1.3): [no log message] 2001-02-14 15:47 eblanco * geneid/src/SearchEvidenceExons.c (1.4): Deleting OFFSET on <= l2 2001-02-13 18:42 eblanco * geneid/src/SearchEvidenceExons.c (1.3): Changing < l2 by <=l2+COFFSET because evidences are into (1,L). 2001-02-08 10:58 eblanco * geneid/src/SortExons.c (1.3): Adding more controls over addition of evidences. 2001-02-07 18:45 eblanco * geneid/include/geneid.h (1.8): New INFI 99 999999 and adding chromosome-sizes defines for sites and exon-types. 2001-02-07 18:37 eblanco * geneid/src/SearchEvidenceExons.c (1.2): adding comment 2001-02-07 18:36 eblanco * geneid/src/geneid.c (1.3): Changing parameters for call SearchingEvidence l2 instead of INFI 2001-02-07 18:28 eblanco * geneid/src/DumpHash.c (1.3): New hash function to be able to process chromosome-size sequences 2000-12-18 10:37 eblanco * geneid/src/BuildORFs.c (1.1): Initial revision 2000-10-10 17:51 eblanco * geneid/src/ScoreExons.c (1.4): Erasing order requirements about SR. For each exon, all the SR(HSP) are read and used. 2000-09-27 15:23 adminmonstre * geneid/README.software_geneid (1.1, geneid_v1_2, v1_1_alpha-2002_03_20): Initial draft for README files on each subdirectory 2000-09-08 12:39 eblanco * geneid/include/geneid.h (1.7): More high evidence value 2000-09-08 12:38 eblanco * geneid/include/geneid.h (1.6): Set 10000 for evidences 2000-09-08 12:11 eblanco * geneid/src/ReadExonsGFF.c (1.5): nothing 2000-09-08 12:10 eblanco * geneid/src/ReadExonsGFF.c (1.4): fixing this concat(strand): /* Concat the strand after the type */ slen = strlen(saux); saux[slen++] = (pv->vExons+i)->Strand; saux[slen] = '\0'; 2000-09-08 12:07 eblanco * geneid/src/Output.c (1.4): Adding e-mail address geneid@imim.es 2000-09-08 11:54 eblanco * geneid/include/geneid.h (1.5): Set NUMEVIDENCES > 0 2000-09-05 12:31 eblanco * geneid/src/ScoreExons.c (1.3): Adding ... [(endexon>OligoLength_1)?endexon-OligoLength_1+1:endexon] to ScoreExons to avoid getting out of range. 2000-09-01 17:54 eblanco * geneid/src/PrintSites.c (1.3): changing %5.3 to %5.2 2000-09-01 17:53 eblanco * geneid/src/PrintExons.c (1.2): Changing %5.3f to %5.2f and AA x - AA x to AA x:x 2000-08-22 12:19 eblanco * geneid/src/CookingGenes.c (1.3): Changing PrintGExon(start,Name,s,dAA,igen,tAA[nExon][0],tAA[nExon][1],nAA); by PrintGExon(end,Name,s,dAA,igen,tAA[nExon][0],tAA[nExon][1],nAA); It isn't important... 2000-08-22 12:12 eblanco * geneid/src/CookingGenes.c (1.2): Sorted Printing (Extended flag) PrintSite(start->Acceptor,type1,Name,strand,s,p1); PrintGExon(start,Name,s,dAA,igen,tAA[nExon][0],tAA[nExon][1],nAA); PrintSite(start->Donor,type2,Name,strand,s,p2); 2000-08-22 11:44 eblanco * geneid/src/ScoreExons.c (1.2): Fixing alpha-bug: isochores[currentIsochore]->OligoDistTran[j][(iniexon)?iniexon-1:0]; -------------------------- 2000-08-16 09:45 eblanco * geneid/src/readparam.c (1.3): adding geneid@imim.es 2000-08-08 16:25 eblanco * geneid/src/readparam.c (1.2): if (nIsochores > xxx) 2000-08-08 16:24 eblanco * geneid/src/geneid.c (1.2): Adding free() 2000-08-08 16:24 eblanco * geneid/src/SortExons.c (1.2): Improving: handling memory 2000-08-08 16:23 eblanco * geneid/src/ScoreExons.c (1.1): Initial revision 2000-08-08 16:22 eblanco * geneid/src/RequestMemory.c (1.3): Adding OligoIni and OligoTran from MarkovScan 2000-08-08 16:22 eblanco * geneid/src/ReadSequence.c (1.2): Fixing behaviour of this routine with alotoffastasequences files 2000-08-08 16:20 eblanco * geneid/src/ReadSR.c (1.2): Allow to use SR with a-lot-of-fasta-sequences files 2000-08-08 16:19 eblanco * geneid/src/ReadExonsGFF.c (1.3): Improving INPUT of data 2000-08-08 16:19 eblanco * geneid/src/PrintExons.c (1.1): Initial revision 2000-08-08 16:18 eblanco * geneid/src/Output.c (1.3): Improving output headers 2000-08-08 16:17 eblanco * geneid/src/GetStopCodons.c (1.2): Including NUMSITES var 2000-08-08 16:17 eblanco * geneid/src/GetSitesWithProfile.c (1.2): Adding NUMSITES var 2000-08-08 16:16 eblanco * geneid/src/DumpHash.c (1.2): Improving of freeing dumpnodes 2000-08-08 16:16 eblanco * geneid/src/BuildTerminalExons.c (1.2): including exon-type ratios 2000-08-08 16:15 eblanco * geneid/src/: BuildInternalExons.c (1.2), BuildSingles.c (1.2): Including exon-type ratios 2000-08-08 16:15 eblanco * geneid/src/BuildInitialExons.c (1.2): Including exon-type RATIO 2000-08-08 16:14 eblanco * geneid/include/geneid.h (1.4): new exon-type RATIOS 2000-07-28 12:56 eblanco * geneid/src/ReadExonsGFF.c (1.2): adding pv->nvSites =0 for many-sequences files 2000-07-26 10:25 eblanco * geneid/src/BackupGenes.c (1.2): ADDING... if (MAXBACKUPSITES && MAXBACKUPEXONS) 2000-07-26 09:59 eblanco * geneid/src/RequestMemory.c (1.2): [no log message] 2000-07-26 09:55 eblanco * geneid/include/geneid.h (1.3): Last changes before distribution(ratios) 2000-07-26 09:54 eblanco * geneid/src/account.c (1.2): Verify LENGTHSi > OVERLAP. 2000-07-21 13:40 eblanco * geneid/include/geneid.h (1.2): Increasing BACKUP values 2000-07-18 20:03 eblanco * geneid/src/geneid.c (1.1): Initial revision 2000-07-18 20:00 eblanco * geneid/include/geneid.h (1.1): Initial revision 2000-07-12 14:09 eblanco * geneid/src/genamic.c (1.3): Adding this flag for get more speed, if ((pg->Ga[etype][frame]->Strand !='*') && when DMAX restriction is checked. 2000-07-11 10:54 eblanco * geneid/src/genamic.c (1.2): change geneId to geneid 2000-07-07 22:28 eblanco * geneid/src/PrintSites.c (1.2): Do not print the group 0 2000-07-07 12:44 eblanco * geneid/src/readparam.c (1.1): Initial revision 2000-07-07 12:37 eblanco * geneid/src/ReadExonsGFF.c (1.1): Initial revision 2000-07-07 10:20 eblanco * geneid/src/: BuildInitialExons.c (1.1), BuildInternalExons.c (1.1), BuildTerminalExons.c (1.1), BuildSingles.c (1.1): Initial revision 2000-07-05 11:10 eblanco * geneid/src/RequestMemory.c (1.1): Initial revision 2000-07-05 10:49 eblanco * geneid/src/Output.c (1.2): New output header 2000-07-05 10:32 eblanco * geneid/src/: Translate.c (1.1), account.c (1.1), genamic.c (1.1), readargv.c (1.1): Initial revision 2000-07-05 10:26 eblanco * geneid/src/: SearchEvidenceExons.c (1.1), SortExons.c (1.1), SwitchFrames.c (1.1), SwitchPositions.c (1.1): Initial revision 2000-07-05 10:22 eblanco * geneid/src/: ReadGeneModel.c (1.1), ReadSR.c (1.1), ReadSequence.c (1.1), RecomputePositions.c (1.1): Initial revision 2000-07-05 10:18 eblanco * geneid/src/: Output.c (1.1), PrintSites.c (1.1): Initial revision 2000-07-05 10:15 eblanco * geneid/src/: FetchSequence.c (1.1), GetStopCodons.c (1.1): Initial revision 2000-07-05 10:12 eblanco * geneid/src/: Dictionary.c (1.1), DumpHash.c (1.1), GetSitesWithProfile.c (1.1): Initial revision 2000-07-05 10:08 eblanco * geneid/src/: CookingGenes.c (1.1), CorrectExon.c (1.1): Initial revision 2000-07-05 09:54 eblanco * geneid/src/BuildSort.c (1.1): Initial revision 2000-07-05 09:46 eblanco * geneid/src/BackupGenes.c (1.1): Initial revision