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• 22:13, 17 November 2010 (diff | hist) . . (-465)‎ . . Software ‎ (Undo revision 2523 by Upugema (Talk))
• 16:21, 17 November 2010 (diff | hist) . . (-22)‎ . . LibStatGen: GLF ‎
• 16:20, 17 November 2010 (diff | hist) . . (-22)‎ . . LibStatGen: FASTQ ‎
• 16:20, 17 November 2010 (diff | hist) . . (-22)‎ . . C++ Class: FastQFile ‎
• 16:18, 17 November 2010 (diff | hist) . . (-22)‎ . . C++ Class: SamRecord ‎
• 16:18, 17 November 2010 (diff | hist) . . (-22)‎ . . C++ Class: SamFileHeader ‎
• 16:16, 17 November 2010 (diff | hist) . . (-22)‎ . . C++ Class: SamFile ‎
• 16:16, 17 November 2010 (diff | hist) . . (-22)‎ . . LibStatGen: BAM ‎
• 16:15, 17 November 2010 (diff | hist) . . (-22)‎ . . C++ Class: CigarRoller ‎
• 16:14, 17 November 2010 (diff | hist) . . (-22)‎ . . C++ Class: InputFile ‎
• 16:14, 17 November 2010 (diff | hist) . . (-22)‎ . . LibStatGen: general ‎
• 16:13, 17 November 2010 (diff | hist) . . (+10)‎ . . C++ Library: libStatGen ‎
• 14:41, 17 November 2010 (diff | hist) . . (+31)‎ . . LibStatGen Download ‎
• 14:35, 17 November 2010 (diff | hist) . . (+26)‎ . . FastQValidator ‎
• 14:33, 17 November 2010 (diff | hist) . . (+411)‎ . . FastQValidator ‎
• 14:32, 17 November 2010 (diff | hist) . . (0)‎ . . File:StatGen.0.1.2.tgz ‎ (uploaded a new version of "File:StatGen.0.1.2.tgz": Quick fix to update the usage for fastqValidator) (current)
• 14:24, 17 November 2010 (diff | hist) . . (0)‎ . . File:StatGen.0.1.2.tgz ‎ (uploaded a new version of "File:StatGen.0.1.2.tgz")
• 14:20, 17 November 2010 (diff | hist) . . (0)‎ . . N File:StatGen.0.1.2.tgz ‎
• 14:19, 17 November 2010 (diff | hist) . . (+94)‎ . . LibStatGen Download ‎
• 14:17, 17 November 2010 (diff | hist) . . (-119)‎ . . LibStatGen Download ‎
• 14:17, 17 November 2010 (diff | hist) . . (0)‎ . . LibStatGen Download ‎
• 14:17, 17 November 2010 (diff | hist) . . (+854)‎ . . LibStatGen Download ‎
• 17:19, 12 November 2010 (diff | hist) . . (+81)‎ . . C++ Library: libStatGen ‎
• 17:11, 12 November 2010 (diff | hist) . . (+210)‎ . . LibStatGen: GLF ‎
• 16:50, 12 November 2010 (diff | hist) . . (-2)‎ . . LibStatGen: GLF ‎
• 16:49, 12 November 2010 (diff | hist) . . (+44)‎ . . LibStatGen: GLF ‎
• 12:07, 12 November 2010 (diff | hist) . . (+49)‎ . . Software ‎
• 13:46, 9 November 2010 (diff | hist) . . (-112)‎ . . LibStatGen Download ‎
• 13:00, 9 November 2010 (diff | hist) . . (0)‎ . . N File:StatGen.0.1.1.tgz ‎ (current)
• 12:59, 9 November 2010 (diff | hist) . . (+196)‎ . . LibStatGen Download ‎
• 14:14, 8 November 2010 (diff | hist) . . (-1)‎ . . Software ‎
• 14:14, 8 November 2010 (diff | hist) . . (+18)‎ . . Software ‎
• 14:13, 8 November 2010 (diff | hist) . . (+94)‎ . . Software ‎
• 14:12, 8 November 2010 (diff | hist) . . (0)‎ . . N File:TrostASHG2010.pdf ‎ (current)
• 13:27, 8 November 2010 (diff | hist) . . (+64)‎ . . LibStatGen Download ‎
• 12:58, 8 November 2010 (diff | hist) . . (+544)‎ . . N LibStatGen Download ‎ (Created page with ' == Download == Click the link to download the tar of the statgen library and tools: StatGen.0.1.0.tgz '''If you use this software, please e-mail me,…')
• 12:56, 8 November 2010 (diff | hist) . . (-325)‎ . . Software ‎
• 02:37, 2 November 2010 (diff | hist) . . (+37)‎ . . LibStatGen: GLF ‎
• 02:23, 2 November 2010 (diff | hist) . . (+31)‎ . . N Category:LibStatGen GLF ‎ (Created page with 'StatGen classes relating to GLF') (current)
• 02:22, 2 November 2010 (diff | hist) . . (-3)‎ . . LibStatGen: BAM ‎
• 02:21, 2 November 2010 (diff | hist) . . (+1,253)‎ . . N LibStatGen: GLF ‎ (Created page with 'Category:Software Category:C++ Category:libStatGen Category:libStatGen GLF = GLF = === GLF Classes === {| style="margin: 1em 1em 1em 0; background-color: #f9f9f…')
• 02:16, 2 November 2010 (diff | hist) . . (+1)‎ . . C++ Library: libStatGen ‎
• 02:15, 2 November 2010 (diff | hist) . . (+198)‎ . . C++ Library: libStatGen ‎ (→‎Download)
• 02:13, 2 November 2010 (diff | hist) . . (0)‎ . . N File:StatGen.0.1.0.tgz ‎ (current)
• 02:11, 2 November 2010 (diff | hist) . . (-26)‎ . . BamUtil: validate ‎
• 02:11, 2 November 2010 (diff | hist) . . (-13)‎ . . BamUtil ‎
• 02:10, 2 November 2010 (diff | hist) . . (+40)‎ . . Software ‎
• 02:08, 2 November 2010 (diff | hist) . . (0)‎ . . BamUtil ‎
• 02:07, 2 November 2010 (diff | hist) . . (-13)‎ . . BamUtil ‎
• 02:06, 2 November 2010 (diff | hist) . . (+44)‎ . . BamUtil ‎
• 02:05, 2 November 2010 (diff | hist) . . (+28)‎ . . BamUtil: validate ‎
• 02:04, 2 November 2010 (diff | hist) . . (-349)‎ . . BamUtil: validate ‎
• 02:03, 2 November 2010 (diff | hist) . . (+347)‎ . . Software ‎
• 02:00, 2 November 2010 (diff | hist) . . (+54)‎ . . C++ Class: CigarRoller ‎
• 01:59, 2 November 2010 (diff | hist) . . (0)‎ . . N File:StatGen 0.1.0.tgz ‎ (current)
• 01:58, 2 November 2010 (diff | hist) . . (+58)‎ . . C++ Class: InputFile ‎
• 01:56, 2 November 2010 (diff | hist) . . (+52)‎ . . N Category:LibStatGen general ‎ (Created page with 'part of the general directory of the statgen library') (current)
• 01:56, 2 November 2010 (diff | hist) . . (+57)‎ . . C++ Library: general Change Log ‎
• 01:56, 2 November 2010 (diff | hist) . . (+52)‎ . . C++ Library: general Change Log ‎
• 01:55, 2 November 2010 (diff | hist) . . (+45)‎ . . N C++ Library: libcsg Change Log ‎ (moved C++ Library: libcsg Change Log to C++ Library: general Change Log) (current)
• 01:55, 2 November 2010 (diff | hist) . . (0)‎ . . m C++ Library: general Change Log ‎ (moved C++ Library: libcsg Change Log to C++ Library: general Change Log)
• 01:55, 2 November 2010 (diff | hist) . . (+76)‎ . . LibStatGen: general ‎
• 01:53, 2 November 2010 (diff | hist) . . (+37)‎ . . N C++ Library: libcsg ‎ (moved C++ Library: libcsg to StatGenLibrary: general) (current)
• 01:53, 2 November 2010 (diff | hist) . . (0)‎ . . m LibStatGen: general ‎ (moved C++ Library: libcsg to StatGenLibrary: general)
• 01:50, 2 November 2010 (diff | hist) . . (+68)‎ . . C++ Class: SamRecord ‎
• 01:50, 2 November 2010 (diff | hist) . . (+68)‎ . . C++ Class: SamFileHeader ‎
• 01:49, 2 November 2010 (diff | hist) . . (+92)‎ . . C++ Class: SamFile ‎
• 01:48, 2 November 2010 (diff | hist) . . (+53)‎ . . Sam Library Usage Examples ‎
• 01:48, 2 November 2010 (diff | hist) . . (+53)‎ . . SAM/BAM Classes FAQs ‎
• 01:47, 2 November 2010 (diff | hist) . . (+53)‎ . . BAM Review Action Items ‎
• 01:46, 2 November 2010 (diff | hist) . . (+47)‎ . . N Category:LibStatGen BAM ‎ (Created page with 'Part of the BAM portion of the statGen library.') (current)
• 01:45, 2 November 2010 (diff | hist) . . (+34)‎ . . N SAM/BAM Library FAQs ‎ (moved SAM/BAM Library FAQs to SAM/BAM Classes FAQs) (current)
• 01:45, 2 November 2010 (diff | hist) . . (0)‎ . . m SAM/BAM Classes FAQs ‎ (moved SAM/BAM Library FAQs to SAM/BAM Classes FAQs)
• 01:44, 2 November 2010 (diff | hist) . . (+27)‎ . . LibStatGen: BAM ‎
• 01:44, 2 November 2010 (diff | hist) . . (+47)‎ . . N Category:LibStatGen FASTQ ‎ (Created page with 'Part of the FASTQ folder of the StatGen Library') (current)
• 01:43, 2 November 2010 (diff | hist) . . (+94)‎ . . C++ Class: FastQFile ‎
• 01:43, 2 November 2010 (diff | hist) . . (+55)‎ . . C++ Library: FASTQ Change Log ‎
• 01:43, 2 November 2010 (diff | hist) . . (+34)‎ . . N Category:LibStatGen ‎ (Created page with 'These pages are part of libStatGen') (current)
• 01:42, 2 November 2010 (diff | hist) . . (+64)‎ . . C++ Library: libStatGen ‎
• 01:42, 2 November 2010 (diff | hist) . . (+94)‎ . . LibStatGen: FASTQ ‎
• 01:40, 2 November 2010 (diff | hist) . . (-26)‎ . . FastQValidator ‎
• 01:34, 2 November 2010 (diff | hist) . . (-361)‎ . . LibStatGen: BAM ‎
• 01:32, 2 November 2010 (diff | hist) . . (+2)‎ . . C++ Library: FASTQ Change Log ‎
• 01:32, 2 November 2010 (diff | hist) . . (+50)‎ . . C++ Library: FASTQ Change Log ‎
• 01:31, 2 November 2010 (diff | hist) . . (-3)‎ . . LibStatGen: FASTQ ‎ (→‎Library Output)
• 01:31, 2 November 2010 (diff | hist) . . (+11)‎ . . LibStatGen: FASTQ ‎
• 01:18, 2 November 2010 (diff | hist) . . (+20)‎ . . LibStatGen: FASTQ ‎
• 01:17, 2 November 2010 (diff | hist) . . (+43)‎ . . N C++ Library: libfqf Change Log ‎ (moved C++ Library: libfqf Change Log to C++ Library: FASTQ Change Log) (current)
• 01:17, 2 November 2010 (diff | hist) . . (0)‎ . . m C++ Library: FASTQ Change Log ‎ (moved C++ Library: libfqf Change Log to C++ Library: FASTQ Change Log)
• 01:14, 2 November 2010 (diff | hist) . . (-1)‎ . . LibStatGen: FASTQ ‎ (→‎FastQValidator)
• 01:13, 2 November 2010 (diff | hist) . . (-319)‎ . . LibStatGen: FASTQ ‎
• 01:11, 2 November 2010 (diff | hist) . . (+2,517)‎ . . Software ‎
• 00:35, 2 November 2010 (diff | hist) . . (+53)‎ . . VcfGenomeStat ‎ (current)
• 00:19, 2 November 2010 (diff | hist) . . (+1,040)‎ . . N VcfGenomeStat ‎ (Created page with '== Purpose == vcfGenomeStat - print flanking sequences and how often they appear for input vcf file. == Usage == <pre> ../bin/vcfGenomeStat [-L <integer>] [-w <integer>] [-l…')
• 18:47, 1 November 2010 (diff | hist) . . (0)‎ . . BamUtil: splitBam ‎
• 18:44, 1 November 2010 (diff | hist) . . (+32)‎ . . BamUtil: splitBam ‎
• 18:39, 1 November 2010 (diff | hist) . . (+876)‎ . . N BamUtil: splitBam ‎ (Created page with '== SplitBam == Split a BAM file into multiple BAM files based on ReadGroup according to the following details. # Creates multiple output files named [outprefix].[RGID].bam, for e…')
• 18:37, 1 November 2010 (diff | hist) . . (+79)‎ . . BamUtil: mergeBam ‎
• 18:31, 1 November 2010 (diff | hist) . . (+4)‎ . . BamUtil: mergeBam ‎
• 18:30, 1 November 2010 (diff | hist) . . (-4)‎ . . BamUtil: mergeBam ‎
• 18:29, 1 November 2010 (diff | hist) . . (+10)‎ . . BamUtil: mergeBam ‎
• 18:29, 1 November 2010 (diff | hist) . . (-65)‎ . . BamUtil: mergeBam ‎
• 18:29, 1 November 2010 (diff | hist) . . (+359)‎ . . BamUtil: mergeBam ‎
• 18:05, 1 November 2010 (diff | hist) . . (-1)‎ . . BamUtil: mergeBam ‎
• 17:42, 1 November 2010 (diff | hist) . . (+70)‎ . . BamUtil: mergeBam ‎
• 17:40, 1 November 2010 (diff | hist) . . (+796)‎ . . N BamUtil: mergeBam ‎ (Created page with ' rgMergeBam merges multiple sorted BAM files into one BAM file like 'samtools merge' command, but merges BAM headers. * Checks that the HD and SQ tags are identical across the BA…')
• 17:34, 1 November 2010 (diff | hist) . . (+2,840)‎ . . N Pileup ‎ (Created page with ' Features: # Option to include a VCF file to select chromosome locations of interest #* Input VCF file can be gzipped or plain text. #*The output VCF file when an input VCF file …')
• 16:21, 1 November 2010 (diff | hist) . . (+3,542)‎ . . BamUtil: polishBam ‎
• 15:21, 29 October 2010 (diff | hist) . . (-56)‎ . . BamUtil: polishBam ‎
• 14:47, 29 October 2010 (diff | hist) . . (-52)‎ . . BamUtil: polishBam ‎
• 14:46, 29 October 2010 (diff | hist) . . (+379)‎ . . BamUtil: polishBam ‎
• 14:42, 29 October 2010 (diff | hist) . . (+917)‎ . . N BamUtil: polishBam ‎ (Created page with '== Trim BAM == The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. <code>trimBam</code> trims the end of reads in a SAM/BAM file, chang…')
• 14:40, 29 October 2010 (diff | hist) . . (+40)‎ . . N Category:BAM Software ‎ (Created page with 'Software tools that work with BAM files.')
• 14:40, 29 October 2010 (diff | hist) . . (+26)‎ . . BamUtil: trimBam ‎
• 14:40, 29 October 2010 (diff | hist) . . (+86)‎ . . N Category:StatGen Download ‎ (Created page with 'These are the tools and library classes that are downloaded with the statgen download.') (current)
• 14:39, 29 October 2010 (diff | hist) . . (+24)‎ . . BamUtil: trimBam ‎
• 14:38, 29 October 2010 (diff | hist) . . (+867)‎ . . N BamUtil: trimBam ‎ (Created page with '== Trim BAM == The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. <code>trimBam</code> trims the end of reads in a SAM/BAM file, chang…')
• 13:33, 29 October 2010 (diff | hist) . . (0)‎ . . C++ Library: libStatGen ‎
• 13:33, 29 October 2010 (diff | hist) . . (+843)‎ . . C++ Library: libStatGen ‎
• 19:10, 25 October 2010 (diff | hist) . . (+42)‎ . . N C++ Library: libStatGen ‎ (Created page with 'To use the StatGenLibrary, first download:')
• 12:02, 25 October 2010 (diff | hist) . . (+207)‎ . . FastQValidator ‎
• 11:47, 25 October 2010 (diff | hist) . . (+35)‎ . . N C++ Library: libfqf ‎ (moved C++ Library: libfqf to StatGenLibrary: FASTQ) (current)
• 11:47, 25 October 2010 (diff | hist) . . (0)‎ . . m LibStatGen: FASTQ ‎ (moved C++ Library: libfqf to StatGenLibrary: FASTQ)
• 11:42, 25 October 2010 (diff | hist) . . (+33)‎ . . N C++ Library: libbam ‎ (moved C++ Library: libbam to StatGenLibrary: BAM) (current)
• 11:42, 25 October 2010 (diff | hist) . . (0)‎ . . m LibStatGen: BAM ‎ (moved C++ Library: libbam to StatGenLibrary: BAM)
• 13:01, 13 October 2010 (diff | hist) . . (-136)‎ . . BamUtil: filter ‎
• 13:00, 13 October 2010 (diff | hist) . . (-643)‎ . . BamUtil ‎
• 12:58, 13 October 2010 (diff | hist) . . (-721)‎ . . BamUtil: validate ‎
• 12:57, 13 October 2010 (diff | hist) . . (+520)‎ . . BamUtil ‎
• 12:15, 11 October 2010 (diff | hist) . . (-1)‎ . . C++ Class: CigarRoller ‎ (→‎Cigar)
• 11:58, 8 October 2010 (diff | hist) . . (-3,136)‎ . . Sam Library Usage Examples ‎
• 17:29, 30 September 2010 (diff | hist) . . (+2,583)‎ . . BamUtil: filter ‎
• 17:11, 30 September 2010 (diff | hist) . . (+1,364)‎ . . BamUtil: filter ‎
• 16:30, 30 September 2010 (diff | hist) . . (+129)‎ . . BamUtil: filter ‎
• 16:29, 30 September 2010 (diff | hist) . . (+575)‎ . . BamUtil: filter ‎
• 16:24, 30 September 2010 (diff | hist) . . (+698)‎ . . BamUtil: filter ‎
• 15:58, 30 September 2010 (diff | hist) . . (+408)‎ . . BamUtil: filter ‎
• 15:55, 30 September 2010 (diff | hist) . . (+637)‎ . . BamUtil: filter ‎
• 15:51, 30 September 2010 (diff | hist) . . (+1,175)‎ . . BamUtil: filter ‎
• 15:18, 30 September 2010 (diff | hist) . . (+1,247)‎ . . N BamUtil: filter ‎ (Created page with 'Category:libbam == filter == The <code>filter</code> option on the bam executable writes the alignments filtering them by clipping ends with too high of a mismatch …')
• 15:15, 30 September 2010 (diff | hist) . . (+585)‎ . . BamUtil ‎
• 15:05, 30 September 2010 (diff | hist) . . (+271)‎ . . BamUtil ‎
• 15:01, 30 September 2010 (diff | hist) . . (+1,033)‎ . . BamUtil ‎
• 11:34, 30 September 2010 (diff | hist) . . (+100)‎ . . BamUtil ‎
• 18:52, 29 September 2010 (diff | hist) . . (+39)‎ . . LibStatGen: BAM ‎
• 18:44, 29 September 2010 (diff | hist) . . (+147)‎ . . N Category:C++ ‎ (Created page with 'If you create a page for C++ software, add <pre>Category:C++</pre> to the bottom of the page so that it will automatically be included here.') (current)
• 18:37, 29 September 2010 (diff | hist) . . (+129)‎ . . C++ Class: CigarRoller ‎ (→‎Public Methods)
• 18:36, 29 September 2010 (diff | hist) . . (+11)‎ . . C++ Class: CigarRoller ‎ (→‎Public Methods)
• 18:35, 29 September 2010 (diff | hist) . . (+135)‎ . . C++ Class: CigarRoller ‎ (→‎Public Methods)
• 18:08, 29 September 2010 (diff | hist) . . (+14)‎ . . C++ Class: CigarRoller ‎ (→‎static Methods)
• 18:08, 29 September 2010 (diff | hist) . . (+568)‎ . . C++ Class: CigarRoller ‎
• 18:05, 29 September 2010 (diff | hist) . . (+3)‎ . . C++ Class: CigarRoller ‎ (→‎Public Methods)
• 18:04, 29 September 2010 (diff | hist) . . (+151)‎ . . C++ Class: CigarRoller ‎ (→‎Public Methods)
• 18:03, 29 September 2010 (diff | hist) . . (+147)‎ . . LibStatGen: general ‎
• 17:50, 29 September 2010 (diff | hist) . . (-22)‎ . . C++ Class: InputFile ‎
• 17:50, 29 September 2010 (diff | hist) . . (-22)‎ . . C++ Class: CigarRoller ‎
• 17:48, 29 September 2010 (diff | hist) . . (+156)‎ . . N Category:Libcsg ‎ (Created page with 'If you create a page for software in libcsg, add <pre>Category:libcsg</pre> to the bottom of the page so that it will automatically be included here.') (current)
• 17:47, 29 September 2010 (diff | hist) . . (+61)‎ . . C++ Class: CigarRoller ‎
• 17:46, 29 September 2010 (diff | hist) . . (+61)‎ . . LibStatGen: general ‎
• 17:45, 29 September 2010 (diff | hist) . . (+60)‎ . . C++ Class: InputFile ‎
• 17:44, 29 September 2010 (diff | hist) . . (+978)‎ . . C++ Library: general Change Log ‎
• 17:28, 29 September 2010 (diff | hist) . . (+201)‎ . . C++ Class: InputFile ‎
• 17:26, 29 September 2010 (diff | hist) . . (+434)‎ . . C++ Class: InputFile ‎ (→‎Example)
• 17:21, 29 September 2010 (diff | hist) . . (+2,197)‎ . . C++ Class: InputFile ‎
• 16:12, 29 September 2010 (diff | hist) . . (+27)‎ . . C++ Class: InputFile ‎ (→‎InputFile / IFILE)
• 17:25, 21 September 2010 (diff | hist) . . (+346)‎ . . SAM: Filtering Reads ‎ (current)
• 17:20, 21 September 2010 (diff | hist) . . (+3,316)‎ . . N SAM: Filtering Reads ‎ (Created page with 'Two filters have been requested for updating a SAM/BAM File. A program should be written that will run both at the same time and produce an updated SAM/BAM File. # Sum the qual…')
• 14:55, 20 September 2010 (diff | hist) . . (+32)‎ . . BAM Review Action Items ‎ (→‎Notes)
• 14:45, 20 September 2010 (diff | hist) . . (+92)‎ . . BAM Review Action Items ‎
• 14:25, 20 September 2010 (diff | hist) . . (+319)‎ . . BAM Review Action Items ‎ (→‎Accessing String Values)
• 14:10, 20 September 2010 (diff | hist) . . (+38)‎ . . BAM Review Action Items ‎
• 15:42, 17 September 2010 (diff | hist) . . (+156)‎ . . BAM Review Action Items ‎ (→‎NOTES From Meeting)
• 15:30, 17 September 2010 (diff | hist) . . (-23)‎ . . BAM Review Action Items ‎
• 13:43, 17 September 2010 (diff | hist) . . (+251)‎ . . BAM Review Action Items ‎
• 13:00, 17 September 2010 (diff | hist) . . (+382)‎ . . BAM Review Action Items ‎ (→‎Accessing String Values)
• 12:42, 17 September 2010 (diff | hist) . . (+313)‎ . . BAM Review Action Items ‎
• 12:32, 17 September 2010 (diff | hist) . . (-1)‎ . . BamUtil ‎ (→‎Usage)
• 12:27, 17 September 2010 (diff | hist) . . (+93)‎ . . BAM Review Action Items ‎ (→‎Review Sept 17th)
• 12:17, 17 September 2010 (diff | hist) . . (+1)‎ . . BAM Review Action Items ‎
• 10:16, 17 September 2010 (diff | hist) . . (+3,889)‎ . . BAM Review Action Items ‎
• 09:50, 17 September 2010 (diff | hist) . . (+200)‎ . . BAM Review Action Items ‎
• 09:43, 17 September 2010 (diff | hist) . . (+37)‎ . . BAM Review Action Items ‎
• 09:43, 17 September 2010 (diff | hist) . . (+1,684)‎ . . BAM Review Action Items ‎
• 08:36, 17 September 2010 (diff | hist) . . (+52)‎ . . BAM Review Action Items ‎
• 15:51, 27 August 2010 (diff | hist) . . (+258)‎ . . SAM Validation Criteria ‎ (current)
• 10:38, 26 August 2010 (diff | hist) . . (+70)‎ . . C++ Class: SamFile ‎ (→‎Statistic Generation)
• 17:22, 23 August 2010 (diff | hist) . . (+293)‎ . . C++ Class: SamFile ‎
• 17:20, 23 August 2010 (diff | hist) . . (-1)‎ . . C++ Class: SamFile ‎
• 17:19, 23 August 2010 (diff | hist) . . (+336)‎ . . C++ Class: SamFile ‎ (→‎Statistic Generation)
• 17:00, 23 August 2010 (diff | hist) . . (+183)‎ . . BamUtil: validate ‎
• 16:59, 23 August 2010 (diff | hist) . . (+69)‎ . . C++ Class: SamFile ‎ (→‎Statistics)
• 14:34, 23 August 2010 (diff | hist) . . (-2,504)‎ . . BamUtil: validate ‎
• 14:33, 23 August 2010 (diff | hist) . . (+2,597)‎ . . C++ Class: SamFile ‎
• 09:00, 11 August 2010 (diff | hist) . . (+1,620)‎ . . C++ Class: CigarRoller ‎
• 08:39, 11 August 2010 (diff | hist) . . (-12)‎ . . SAM/BAM Classes FAQs ‎
• 08:38, 11 August 2010 (diff | hist) . . (+307)‎ . . C++ Library: general Change Log ‎
• 08:35, 11 August 2010 (diff | hist) . . (+307)‎ . . C++ Class: SamRecord ‎
• 08:32, 11 August 2010 (diff | hist) . . (+668)‎ . . C++ Class: SamRecord ‎
• 08:19, 11 August 2010 (diff | hist) . . (+378)‎ . . C++ Class: SamFile ‎
• 11:11, 4 August 2010 (diff | hist) . . (+70)‎ . . CigarRoller Proposed Update ‎ (current)
• 11:03, 4 August 2010 (diff | hist) . . (+261)‎ . . CigarRoller Proposed Update ‎ (→‎How would this be used by SamRecord)
• 11:00, 4 August 2010 (diff | hist) . . (+634)‎ . . CigarRoller Proposed Update ‎
• 10:52, 4 August 2010 (diff | hist) . . (+3,995)‎ . . N CigarRoller Proposed Update ‎ (Created page with '* Should we rename CigarRoller to Cigar? * Should we be consistent in upper-case vs lower-case first letter of method names? * Should Cigar require a start position? ** I would l…')
• 16:39, 3 August 2010 (diff | hist) . . (+211)‎ . . C++ Class: CigarRoller ‎
• 16:36, 3 August 2010 (diff | hist) . . (+1,449)‎ . . C++ Class: CigarRoller ‎
• 13:19, 3 August 2010 (diff | hist) . . (+983)‎ . . C++ Class: CigarRoller ‎
• 12:49, 3 August 2010 (diff | hist) . . (+14)‎ . . BAM Review Action Items ‎
• 12:47, 3 August 2010 (diff | hist) . . (+206)‎ . . C++ Class: SamFile ‎
• 11:51, 3 August 2010 (diff | hist) . . (+1,016)‎ . . C++ Class: CigarRoller ‎ (→‎Mapping Between Reference and Read/Query)
• 11:39, 3 August 2010 (diff | hist) . . (+997)‎ . . C++ Class: CigarRoller ‎
• 11:22, 3 August 2010 (diff | hist) . . (+428)‎ . . C++ Library: general Change Log ‎
• 12:27, 2 August 2010 (diff | hist) . . (+2,075)‎ . . N C++ Class Averages ‎ (Created page with '<source lang="cpp"> // Static method that returns the mean, meadian, and mode for this dataset. void Average::calculateAverages(double& mean, doub…') (current)
• 11:37, 2 August 2010 (diff | hist) . . (+358)‎ . . C++ Class: CigarRoller ‎
• 11:33, 2 August 2010 (diff | hist) . . (+84)‎ . . SAM/BAM Classes FAQs ‎
• 11:32, 2 August 2010 (diff | hist) . . (+63)‎ . . SAM/BAM Classes FAQs ‎
• 10:44, 2 August 2010 (diff | hist) . . (+134)‎ . . SAM/BAM Classes FAQs ‎
• 10:42, 2 August 2010 (diff | hist) . . (+4,961)‎ . . Sam Library Usage Examples ‎
• 17:55, 30 July 2010 (diff | hist) . . (+1)‎ . . Introduction to new students ‎ (→‎Data File Formats)
• 17:54, 30 July 2010 (diff | hist) . . (+165)‎ . . Introduction to new students ‎ (→‎Data File Formats)
• 17:53, 30 July 2010 (diff | hist) . . (+45)‎ . . Introduction to new students ‎ (→‎Data File Formats)
• 17:52, 30 July 2010 (diff | hist) . . (+92)‎ . . Introduction to new students ‎ (→‎Data File Formats)
• 17:50, 30 July 2010 (diff | hist) . . (+96)‎ . . Introduction to new students ‎ (→‎Resources)
• 17:39, 30 July 2010 (diff | hist) . . (+3,335)‎ . . SAM ‎
• 16:26, 30 July 2010 (diff | hist) . . (+403)‎ . . SAM ‎
• 13:43, 30 July 2010 (diff | hist) . . (-122)‎ . . SAM ‎
• 13:38, 30 July 2010 (diff | hist) . . (+38)‎ . . SAM ‎
• 13:34, 30 July 2010 (diff | hist) . . (+313)‎ . . SAM ‎
• 13:12, 30 July 2010 (diff | hist) . . (+118)‎ . . SAM ‎
• 11:48, 30 July 2010 (diff | hist) . . (+647)‎ . . SAM ‎
• 11:05, 30 July 2010 (diff | hist) . . (0)‎ . . SAM ‎
• 11:05, 30 July 2010 (diff | hist) . . (+96)‎ . . SAM ‎
• 17:49, 29 July 2010 (diff | hist) . . (+1,063)‎ . . SAM/BAM Classes FAQs ‎
• 17:35, 29 July 2010 (diff | hist) . . (+4)‎ . . C++ Class: SamFile ‎
• 17:26, 29 July 2010 (diff | hist) . . (+8)‎ . . SAM/BAM Classes FAQs ‎
• 17:25, 29 July 2010 (diff | hist) . . (+6)‎ . . SAM/BAM Classes FAQs ‎
• 17:23, 29 July 2010 (diff | hist) . . (+339)‎ . . N SAM/BAM Classes FAQs ‎ (Created page with '== How Do I? == * Map between a query/read sequence and a reference sequence to do things like looking up a base/quality at a given reference position or looking up a reference …')
• 17:18, 29 July 2010 (diff | hist) . . (+37)‎ . . LibStatGen: BAM ‎
• 17:16, 29 July 2010 (diff | hist) . . (+1,593)‎ . . C++ Class: CigarRoller ‎
• 14:34, 29 July 2010 (diff | hist) . . (-1)‎ . . SAM ‎ (→‎What Information Does SAM/BAM Have for an Alignment)
• 14:32, 29 July 2010 (diff | hist) . . (-1)‎ . . SAM ‎
• 14:32, 29 July 2010 (diff | hist) . . (+1,394)‎ . . SAM ‎
• 14:13, 29 July 2010 (diff | hist) . . (+142)‎ . . SAM ‎
• 13:31, 29 July 2010 (diff | hist) . . (+475)‎ . . SAM ‎
• 11:51, 29 July 2010 (diff | hist) . . (+2,359)‎ . . SAM ‎
• 11:15, 29 July 2010 (diff | hist) . . (+2,373)‎ . . SAM ‎
• 16:17, 28 July 2010 (diff | hist) . . (+18)‎ . . BamUtil ‎
• 16:17, 28 July 2010 (diff | hist) . . (+18)‎ . . BamUtil ‎ (→‎readIndexedBam)
• 16:17, 28 July 2010 (diff | hist) . . (+832)‎ . . BamUtil ‎
• 14:49, 23 July 2010 (diff | hist) . . (+117)‎ . . Software ‎ (→‎Validators)
• 11:24, 22 July 2010 (diff | hist) . . (-6)‎ . . BamUtil: validate ‎
• 11:23, 22 July 2010 (diff | hist) . . (+29)‎ . . N File:Bam.0.0.2.tgz ‎ (BAM Validator Initial Release) (current)
• 11:14, 22 July 2010 (diff | hist) . . (+84)‎ . . BamUtil: validate ‎
• 11:13, 22 July 2010 (diff | hist) . . (-83)‎ . . BamUtil: validate ‎
• 11:04, 22 July 2010 (diff | hist) . . (+1)‎ . . BamUtil: validate ‎ (→‎Download)
• 11:04, 22 July 2010 (diff | hist) . . (+82)‎ . . BamUtil: validate ‎ (→‎Download)
• 11:00, 22 July 2010 (diff | hist) . . (+6)‎ . . BamUtil: validate ‎
• 10:42, 22 July 2010 (diff | hist) . . (+63)‎ . . BamUtil: validate ‎ (→‎Status)
• 10:41, 22 July 2010 (diff | hist) . . (+72)‎ . . BamUtil: validate ‎ (→‎Status)
• 10:41, 22 July 2010 (diff | hist) . . (-2,197)‎ . . BamUtil ‎ (→‎validate)
• 10:40, 22 July 2010 (diff | hist) . . (+34)‎ . . LibStatGen: BAM ‎ (→‎Executable)
• 10:00, 22 July 2010 (diff | hist) . . (+27)‎ . . BamUtil: validate ‎
• 09:59, 22 July 2010 (diff | hist) . . (+2)‎ . . BamUtil: validate ‎
• 09:58, 22 July 2010 (diff | hist) . . (+284)‎ . . BamUtil: validate ‎
• 18:27, 21 July 2010 (diff | hist) . . (0)‎ . . BamUtil: validate ‎
• 18:26, 21 July 2010 (diff | hist) . . (+8,720)‎ . . N BamUtil: validate ‎ (Created page with 'BamValidator == Status == The initial version of a SAM/BAM Validator is complete. It can be found at: http://www.sph.umich.edu/csg/mktrost/bam/ == Purpos…')
• 17:36, 21 July 2010 (diff | hist) . . (+5)‎ . . SAM Validation Criteria ‎
• 17:36, 21 July 2010 (diff | hist) . . (+144)‎ . . SAM Validation Criteria ‎
• 17:25, 21 July 2010 (diff | hist) . . (+18)‎ . . Main Page ‎ (→‎Sequence Analysis Tools)
• 17:09, 21 July 2010 (diff | hist) . . (+6)‎ . . SAM Validation Criteria ‎
• 15:37, 21 July 2010 (diff | hist) . . (+192)‎ . . SAM Validation Criteria ‎
• 15:35, 21 July 2010 (diff | hist) . . (+9)‎ . . SAM Validation Criteria ‎
• 12:29, 20 July 2010 (diff | hist) . . (+68)‎ . . SAM Validation Criteria ‎ (→‎SAM Alignment Validation)
• 12:23, 20 July 2010 (diff | hist) . . (+1,420)‎ . . SAM Validation Criteria ‎ (→‎SAM Header Validation Rules)
• 12:46, 16 July 2010 (diff | hist) . . (+295)‎ . . C++ Library: general Change Log ‎
• 19:05, 14 July 2010 (diff | hist) . . (+188)‎ . . C++ Class: SamFile ‎
• 17:32, 14 July 2010 (diff | hist) . . (+1,376)‎ . . C++ Class: SamFile ‎
• 15:57, 14 July 2010 (diff | hist) . . (+6)‎ . . LibStatGen: BAM ‎
• 11:25, 14 July 2010 (diff | hist) . . (+448)‎ . . BamUtil ‎ (→‎validate)
• 14:27, 2 July 2010 (diff | hist) . . (+164)‎ . . C++ Class: SamFileHeader ‎
• 14:16, 2 July 2010 (diff | hist) . . (+333)‎ . . C++ Class: SamFileHeader ‎
• 07:45, 2 July 2010 (diff | hist) . . (+3)‎ . . C++ Class: SamFileHeader ‎
• 14:00, 1 July 2010 (diff | hist) . . (+124)‎ . . C++ Class: SamFileHeader ‎
• 11:48, 1 July 2010 (diff | hist) . . (+1,626)‎ . . C++ Class: SamFileHeader ‎
• 15:39, 30 June 2010 (diff | hist) . . (+1,777)‎ . . BamUtil ‎
• 15:21, 30 June 2010 (diff | hist) . . (+300)‎ . . BamUtil ‎
• 14:10, 30 June 2010 (diff | hist) . . (-14)‎ . . BamUtil ‎
• 12:01, 30 June 2010 (diff | hist) . . (-83)‎ . . BamUtil ‎ (→‎bam Executable)
• 11:28, 30 June 2010 (diff | hist) . . (+188)‎ . . BamUtil ‎
• 11:25, 30 June 2010 (diff | hist) . . (+565)‎ . . C++ Class: SamFile ‎
• 18:05, 23 June 2010 (diff | hist) . . (-975)‎ . . C++ Class: InputFile ‎
• 18:03, 23 June 2010 (diff | hist) . . (+854)‎ . . C++ Library: general Change Log ‎
• 17:42, 14 June 2010 (diff | hist) . . (+2,259)‎ . . BamUtil ‎
• 17:01, 10 June 2010 (diff | hist) . . (+1,541)‎ . . C++ Class: SamFile ‎
• 16:47, 10 June 2010 (diff | hist) . . (+19)‎ . . Sam Library Usage Examples ‎
• 16:47, 10 June 2010 (diff | hist) . . (+88)‎ . . Sam Library Usage Examples ‎
• 16:43, 10 June 2010 (diff | hist) . . (+90)‎ . . BAM Review Action Items ‎
• 15:26, 10 June 2010 (diff | hist) . . (+16)‎ . . BAM Review Action Items ‎
• 14:52, 10 June 2010 (diff | hist) . . (+32)‎ . . BAM Review Action Items ‎
• 14:51, 10 June 2010 (diff | hist) . . (+128)‎ . . BAM Review Action Items ‎
• 14:51, 10 June 2010 (diff | hist) . . (+37)‎ . . Sam Library Usage Examples ‎
• 14:41, 10 June 2010 (diff | hist) . . (-9,068)‎ . . C++ Class: SamFile ‎
• 14:41, 10 June 2010 (diff | hist) . . (-12)‎ . . Sam Library Usage Examples ‎
• 14:40, 10 June 2010 (diff | hist) . . (+9,098)‎ . . N Sam Library Usage Examples ‎ (Created page with '==== Simple Read/Write SAM/BAM files ==== The following example reads in a sam/bam file and writes it out as a sam/bam file. The file format of the input sam/bam is determined b…')
• 14:39, 10 June 2010 (diff | hist) . . (+54)‎ . . LibStatGen: BAM ‎
• 17:03, 9 June 2010 (diff | hist) . . (+730)‎ . . C++ Class: SamFileHeader ‎
• 17:29, 7 June 2010 (diff | hist) . . (+1,913)‎ . . N BAM Review Action Items ‎ (Created page with '* Move the examples from the SamFile wiki page to their own page ** include links from the main library page and the SamFile page. ** look into why the one example have two if ch…')
• 17:21, 7 June 2010 (diff | hist) . . (+29)‎ . . LibStatGen: BAM ‎
• 12:13, 7 June 2010 (diff | hist) . . (-1)‎ . . LibStatGen: BAM ‎ (→‎Read & Write BAM/SAM Library)
• 08:24, 4 June 2010 (diff | hist) . . (+63)‎ . . m LibStatGen: BAM ‎ (→‎Suggested Improvements/Features)
• 10:11, 3 June 2010 (diff | hist) . . (-1)‎ . . C++ Class: SamRecord ‎
• 10:10, 3 June 2010 (diff | hist) . . (+351)‎ . . C++ Class: SamRecord ‎
• 19:02, 2 June 2010 (diff | hist) . . (+318)‎ . . C++ Library: FASTQ Change Log ‎
• 18:59, 2 June 2010 (diff | hist) . . (+14)‎ . . FastQValidator ‎
• 18:58, 2 June 2010 (diff | hist) . . (+28)‎ . . FastQValidator ‎ (→‎Optional Parameters)
• 18:58, 2 June 2010 (diff | hist) . . (+81)‎ . . FastQValidator ‎
• 18:04, 1 June 2010 (diff | hist) . . (+38)‎ . . FastQValidator ‎
• 18:00, 1 June 2010 (diff | hist) . . (+4)‎ . . BamUtil ‎
• 18:00, 1 June 2010 (diff | hist) . . (+43)‎ . . BamUtil ‎
• 17:57, 1 June 2010 (diff | hist) . . (+21)‎ . . C++ Class: SamRecord ‎
• 17:56, 1 June 2010 (diff | hist) . . (+21)‎ . . C++ Class: SamFileHeader ‎
• 17:56, 1 June 2010 (diff | hist) . . (-9)‎ . . LibStatGen: BAM ‎
• 17:55, 1 June 2010 (diff | hist) . . (+21)‎ . . C++ Class: SamFile ‎
• 17:22, 1 June 2010 (diff | hist) . . (+7)‎ . . LibStatGen: BAM ‎
• 17:21, 1 June 2010 (diff | hist) . . (+23)‎ . . LibStatGen: BAM ‎
• 17:24, 24 May 2010 (diff | hist) . . (+604)‎ . . SAM Validation Criteria ‎
• 13:04, 21 May 2010 (diff | hist) . . (+345)‎ . . SAM Validation Criteria ‎
• 12:44, 21 May 2010 (diff | hist) . . (+21)‎ . . BamUtil ‎
• 12:43, 21 May 2010 (diff | hist) . . (+708)‎ . . BamUtil ‎
• 13:02, 20 May 2010 (diff | hist) . . (+112)‎ . . C++ Class: InputFile ‎
• 11:54, 20 May 2010 (diff | hist) . . (+506)‎ . . C++ Class: InputFile ‎
• 11:49, 20 May 2010 (diff | hist) . . (+956)‎ . . C++ Class: InputFile ‎
• 11:43, 20 May 2010 (diff | hist) . . (+404)‎ . . C++ Library: general Change Log ‎
• 18:12, 19 May 2010 (diff | hist) . . (+88)‎ . . SAM Validation Criteria ‎
• 14:47, 19 May 2010 (diff | hist) . . (+14)‎ . . SAM Validation Criteria ‎
• 13:44, 19 May 2010 (diff | hist) . . (+5)‎ . . SAM Validation Criteria ‎
• 13:35, 19 May 2010 (diff | hist) . . (+289)‎ . . SAM Validation Criteria ‎
• 13:24, 19 May 2010 (diff | hist) . . (+498)‎ . . SAM Validation Criteria ‎
• 12:41, 19 May 2010 (diff | hist) . . (+41)‎ . . SAM Validation Criteria ‎
• 12:40, 19 May 2010 (diff | hist) . . (+4)‎ . . SAM Validation Criteria ‎
• 11:52, 19 May 2010 (diff | hist) . . (+24)‎ . . C++ Class: CigarRoller ‎
• 10:37, 19 May 2010 (diff | hist) . . (+58)‎ . . SAM Validation Criteria ‎
• 10:35, 19 May 2010 (diff | hist) . . (+2)‎ . . C++ Class: SamRecord ‎
• 12:21, 18 May 2010 (diff | hist) . . (+73)‎ . . BamUtil ‎
• 12:21, 18 May 2010 (diff | hist) . . (-73)‎ . . C++ Class: SamRecord ‎
• 18:06, 14 May 2010 (diff | hist) . . (+2,532)‎ . . C++ Class: CigarRoller ‎
• 14:55, 13 May 2010 (diff | hist) . . (-2)‎ . . C++ Class: CigarRoller ‎
• 14:44, 13 May 2010 (diff | hist) . . (+3,925)‎ . . N C++ Class: CigarRoller ‎ (Created page with '= CigarRoller= This class is part of libcsg. This purpose of this class is to provide utilities for creating and processing CIGAR strings. == Public Met…')
• 12:58, 13 May 2010 (diff | hist) . . (+114)‎ . . LibStatGen: general ‎
• 12:56, 13 May 2010 (diff | hist) . . (+27)‎ . . C++ Library: general Change Log ‎
• 12:56, 13 May 2010 (diff | hist) . . (+365)‎ . . C++ Library: general Change Log ‎
• 18:01, 11 May 2010 (diff | hist) . . (+67)‎ . . BamUtil ‎
• 17:59, 11 May 2010 (diff | hist) . . (+1,301)‎ . . BamUtil ‎
• 17:53, 11 May 2010 (diff | hist) . . (+160)‎ . . LibStatGen: BAM ‎
• 17:52, 11 May 2010 (diff | hist) . . (+226)‎ . . LibStatGen: BAM ‎ (→‎Classes in the BAM/SAM Library)
• 17:22, 11 May 2010 (diff | hist) . . (+88)‎ . . LibStatGen: BAM ‎ (→‎Classes in the BAM/SAM Library)
• 17:19, 11 May 2010 (diff | hist) . . (+271)‎ . . C++ Class: SamRecord ‎
• 16:22, 11 May 2010 (diff | hist) . . (+71)‎ . . LibStatGen: BAM ‎
• 16:20, 11 May 2010 (diff | hist) . . (+510)‎ . . C++ Class: SamFileHeader ‎
• 16:06, 11 May 2010 (diff | hist) . . (+11)‎ . . C++ Class: SamFile ‎
• 16:05, 11 May 2010 (diff | hist) . . (+4,004)‎ . . C++ Class: SamFile ‎
• 14:57, 11 May 2010 (diff | hist) . . (+1,105)‎ . . C++ Class: SamFile ‎
• 10:52, 11 May 2010 (diff | hist) . . (+259)‎ . . C++ Class: SamFile ‎
• 13:56, 7 May 2010 (diff | hist) . . (-17)‎ . . SAM Validation Criteria ‎
• 13:33, 7 May 2010 (diff | hist) . . (+10)‎ . . SAM Validation Criteria ‎
• 13:34, 6 May 2010 (diff | hist) . . (+298)‎ . . C++ Class: FastQFile ‎
• 13:31, 6 May 2010 (diff | hist) . . (+35)‎ . . C++ Library: FASTQ Change Log ‎
• 13:30, 6 May 2010 (diff | hist) . . (+284)‎ . . C++ Library: FASTQ Change Log ‎
• 17:48, 3 May 2010 (diff | hist) . . (+240)‎ . . C++ Library: general Change Log ‎
• 17:27, 3 May 2010 (diff | hist) . . (+990)‎ . . N C++ Class: InputFile ‎ (Created page with '= InputFile / IFILE = This is our class for file operations. It hides the underlying file structure from the user. That way code can generically open and operate on a file usin…')
• 16:43, 3 May 2010 (diff | hist) . . (+2)‎ . . LibStatGen: general ‎
• 16:43, 3 May 2010 (diff | hist) . . (+392)‎ . . LibStatGen: general ‎
• 12:14, 3 May 2010 (diff | hist) . . (+101)‎ . . C++ Class: SamRecord ‎
• 10:27, 3 May 2010 (diff | hist) . . (+596)‎ . . C++ Class: SamRecord ‎
• 16:34, 30 April 2010 (diff | hist) . . (+102)‎ . . C++ Library: FASTQ Change Log ‎
• 17:53, 28 April 2010 (diff | hist) . . (+20)‎ . . SAM Validation Criteria ‎ (→‎BamFile Classes)
• 16:33, 28 April 2010 (diff | hist) . . (0)‎ . . Main Page ‎ (→‎Sequence Analysis Tools)
• 16:33, 28 April 2010 (diff | hist) . . (+31)‎ . . Main Page ‎ (→‎Sequence Analysis Tools)
• 16:31, 28 April 2010 (diff | hist) . . (+136)‎ . . C++ Class: SamRecord ‎ (→‎Retrieving fields from a SAM/BAM Record)
• 19:27, 20 April 2010 (diff | hist) . . (-1)‎ . . LibStatGen: BAM ‎
• 19:26, 20 April 2010 (diff | hist) . . (+139)‎ . . LibStatGen: BAM ‎
• 19:09, 20 April 2010 (diff | hist) . . (+5,621)‎ . . C++ Class: SamFileHeader ‎
• 18:41, 20 April 2010 (diff | hist) . . (+4,875)‎ . . C++ Class: SamFileHeader ‎
• 18:30, 16 April 2010 (diff | hist) . . (+449)‎ . . SAM Validation Criteria ‎
• 10:35, 15 April 2010 (diff | hist) . . (+139)‎ . . C++ Library: FASTQ Change Log ‎
• 10:33, 15 April 2010 (diff | hist) . . (+31)‎ . . FastQValidator ‎ (→‎Optional Space Options for Raw Sequence (Last one specified is used))
• 10:32, 15 April 2010 (diff | hist) . . (+4)‎ . . FastQ Validation Criteria ‎
• 10:32, 15 April 2010 (diff | hist) . . (+57)‎ . . FastQ Validation Criteria ‎
• 10:31, 15 April 2010 (diff | hist) . . (-54)‎ . . FastQValidator ‎
• 10:30, 15 April 2010 (diff | hist) . . (-1)‎ . . FastQ Validation Criteria ‎
• 10:29, 15 April 2010 (diff | hist) . . (+201)‎ . . FastQ Validation Criteria ‎
• 10:26, 15 April 2010 (diff | hist) . . (-3,234)‎ . . C++ Class: FastQFile ‎
• 10:26, 15 April 2010 (diff | hist) . . (+3,303)‎ . . N FastQ Validation Criteria ‎ (Created page with '== FastQ Sequence Validation Criteria == {| class="wikitable" style="width:100%" |+ style="font-size:150%" |'''Sequence Identifier Line''' ! width="50%"|Validation Criteria ! …')
• 10:24, 15 April 2010 (diff | hist) . . (+90)‎ . . FastQValidator ‎
• 12:43, 13 April 2010 (diff | hist) . . (+45)‎ . . SAM Validation Criteria ‎ (→‎Other Read Validation)
• 09:48, 13 April 2010 (diff | hist) . . (+157)‎ . . C++ Class: SamFileHeader ‎ (→‎Proposed Accessors)
• 18:58, 12 April 2010 (diff | hist) . . (+505)‎ . . C++ Class: SamFileHeader ‎
• 18:13, 12 April 2010 (diff | hist) . . (+344)‎ . . C++ Library: FASTQ Change Log ‎
• 16:06, 12 April 2010 (diff | hist) . . (-18)‎ . . C++ Class: SamRecord ‎
• 17:50, 7 April 2010 (diff | hist) . . (+631)‎ . . C++ Library: FASTQ Change Log ‎
• 10:42, 7 April 2010 (diff | hist) . . (+290)‎ . . FastQValidator ‎
• 20:07, 6 April 2010 (diff | hist) . . (+55)‎ . . C++ Class: SamRecord ‎
• 20:06, 6 April 2010 (diff | hist) . . (+55)‎ . . C++ Class: SamFileHeader ‎
• 20:06, 6 April 2010 (diff | hist) . . (+54)‎ . . C++ Class: SamFile ‎
• 20:03, 6 April 2010 (diff | hist) . . (-29)‎ . . C++ Class: SamFile ‎
• 19:57, 6 April 2010 (diff | hist) . . (+136)‎ . . LibStatGen: BAM ‎
• 19:51, 6 April 2010 (diff | hist) . . (+70)‎ . . Main Page ‎
• 19:50, 6 April 2010 (diff | hist) . . (+49)‎ . . N Talk:FastQ Validator ‎ (moved Talk:FastQ Validator to Talk:C++ Executable: fastQValidator) (current)
• 19:50, 6 April 2010 (diff | hist) . . (0)‎ . . m Talk:FastQValidator ‎ (moved Talk:FastQ Validator to Talk:C++ Executable: fastQValidator)
• 19:50, 6 April 2010 (diff | hist) . . (+44)‎ . . N FastQ Validator ‎ (moved FastQ Validator to C++ Executable: fastQValidator) (current)
• 19:50, 6 April 2010 (diff | hist) . . (0)‎ . . m FastQValidator ‎ (moved FastQ Validator to C++ Executable: fastQValidator)
• 18:35, 6 April 2010 (diff | hist) . . (0)‎ . . C++ Library: general Change Log ‎
• 18:35, 6 April 2010 (diff | hist) . . (+278)‎ . . C++ Library: general Change Log ‎
• 18:34, 6 April 2010 (diff | hist) . . (+304)‎ . . N C++ Library: FASTQ Change Log ‎ (Created page with '=libfqf Change Log = This page tracks the updates/enhancements that have been updated in the git repository. It is primarily used to track the user interface changes, so users c…')
• 18:31, 6 April 2010 (diff | hist) . . (+52)‎ . . C++ Class: FastQFile ‎
• 18:12, 6 April 2010 (diff | hist) . . (-10,036)‎ . . LibStatGen: FASTQ ‎
• 18:12, 6 April 2010 (diff | hist) . . (+28)‎ . . LibStatGen: general ‎ (→‎Classes in the FastQFile Library)
• 18:11, 6 April 2010 (diff | hist) . . (+10,283)‎ . . C++ Class: FastQFile ‎
• 17:40, 6 April 2010 (diff | hist) . . (+950)‎ . . N C++ Class: FastQFile ‎ (Created page with '== Reading/Validating FastQ Files In Your Program == The '''FastQFile''' class allows a user to easily read/validate a fastq file. === Class Methods === {| style="margin: 1em 1…')
• 17:34, 6 April 2010 (diff | hist) . . (+141)‎ . . LibStatGen: FASTQ ‎
• 17:33, 6 April 2010 (diff | hist) . . (+404)‎ . . LibStatGen: FASTQ ‎
• 17:32, 6 April 2010 (diff | hist) . . (+749)‎ . . N LibStatGen: general ‎ (Created page with '= libcsg = This library contains utility classes that are useful for many of the other developed software programs/libraries. See C++ Library: libcsg Change Log for a list o…')
• 17:20, 6 April 2010 (diff | hist) . . (+33)‎ . . N FastQFile ‎ (moved FastQFile to C++ Library: libfqf) (current)
• 17:20, 6 April 2010 (diff | hist) . . (0)‎ . . m LibStatGen: FASTQ ‎ (moved FastQFile to C++ Library: libfqf)
• 17:20, 6 April 2010 (diff | hist) . . (+3)‎ . . LibStatGen: BAM ‎
• 17:19, 6 April 2010 (diff | hist) . . (+33)‎ . . N C++ Library: bam ‎ (moved C++ Library: bam to C++ Library: libbam) (current)
• 17:19, 6 April 2010 (diff | hist) . . (0)‎ . . m LibStatGen: BAM ‎ (moved C++ Library: bam to C++ Library: libbam)
• 17:10, 6 April 2010 (diff | hist) . . (+847)‎ . . BamUtil ‎
• 17:09, 6 April 2010 (diff | hist) . . (-584)‎ . . LibStatGen: BAM ‎
• 17:02, 6 April 2010 (diff | hist) . . (+5)‎ . . LibStatGen: BAM ‎
• 16:56, 6 April 2010 (diff | hist) . . (+391)‎ . . LibStatGen: BAM ‎
• 16:42, 6 April 2010 (diff | hist) . . (+30)‎ . . N BamFile ‎ (moved BamFile to C++ Library: bam) (current)
• 16:42, 6 April 2010 (diff | hist) . . (0)‎ . . m LibStatGen: BAM ‎ (moved BamFile to C++ Library: bam)
• 16:41, 6 April 2010 (diff | hist) . . (+60)‎ . . C++ Class: SamFileHeader ‎
• 16:41, 6 April 2010 (diff | hist) . . (+528)‎ . . C++ Class: SamRecord ‎
• 16:23, 6 April 2010 (diff | hist) . . (+53)‎ . . C++ Class: SamFile ‎
• 16:20, 6 April 2010 (diff | hist) . . (-1,444)‎ . . C++ Class: SamFile ‎
• 13:43, 6 April 2010 (diff | hist) . . (+606)‎ . . BamUtil ‎
• 11:58, 6 April 2010 (diff | hist) . . (+111)‎ . . BamUtil ‎
• 11:57, 6 April 2010 (diff | hist) . . (+661)‎ . . BamUtil ‎
• 11:50, 6 April 2010 (diff | hist) . . (+425)‎ . . N BamUtil ‎ (Created page with '= bam Executable = The bam executable has the following functions. * Read and Validate a SAM/BAM file * Read a SAM/BAM fi…')
• 11:27, 6 April 2010 (diff | hist) . . (+687)‎ . . C++ Class: SamFile ‎ (→‎Class Methods)
• 11:13, 6 April 2010 (diff | hist) . . (+495)‎ . . C++ Class: SamRecord ‎
• 11:10, 6 April 2010 (diff | hist) . . (+9,448)‎ . . N C++ Class: SamRecord ‎ (Created page with '== Setting fields in a SAM/BAM Record == The '''SamRecord''' class contains accessors to set the fields of a SAM/BAM record. They are used for creating a record that is not read…')
• 11:10, 6 April 2010 (diff | hist) . . (-9,183)‎ . . LibStatGen: BAM ‎
• 11:06, 6 April 2010 (diff | hist) . . (+2,135)‎ . . N C++ Class: SamFileHeader ‎ (Created page with '== SamFileHeader == This class allows a user to get/set the fields in a SAM/BAM Header. === Setting fields in the Header === The '''SamFileHeader''' class contains accessors to …')
• 11:03, 6 April 2010 (diff | hist) . . (-1,282)‎ . . LibStatGen: BAM ‎
• 10:56, 6 April 2010 (diff | hist) . . (+573)‎ . . C++ Class: SamFile ‎
• 10:48, 6 April 2010 (diff | hist) . . (+470)‎ . . C++ Class: SamFile ‎
• 10:41, 6 April 2010 (diff | hist) . . (+726)‎ . . C++ Class: SamFile ‎ (→‎Usage Example)
• 10:09, 6 April 2010 (diff | hist) . . (-2)‎ . . C++ Class: SamFile ‎ (→‎Usage Example)
• 10:05, 6 April 2010 (diff | hist) . . (-7,903)‎ . . LibStatGen: BAM ‎ (→‎Reading/Writing SAM/BAM Files In Your Program)
• 10:04, 6 April 2010 (diff | hist) . . (+130)‎ . . C++ Class: SamFile ‎
• 10:00, 6 April 2010 (diff | hist) . . (+34)‎ . . C++ Class: SamFile ‎
• 09:56, 6 April 2010 (diff | hist) . . (+34)‎ . . LibStatGen: BAM ‎
• 09:49, 6 April 2010 (diff | hist) . . (+17)‎ . . LibStatGen: BAM ‎ (→‎Usage Example)
• 09:46, 6 April 2010 (diff | hist) . . (-4)‎ . . C++ Library: general Change Log ‎
• 09:46, 6 April 2010 (diff | hist) . . (-36)‎ . . C++ Library: general Change Log ‎
• 09:46, 6 April 2010 (diff | hist) . . (+7)‎ . . C++ Library: general Change Log ‎ (→‎4/5/2010)
• 09:45, 6 April 2010 (diff | hist) . . (+715)‎ . . N C++ Library: general Change Log ‎ (Created page with '= C++ Library: libcsg Change Log = == Enhancements/Updates/Fixes == === 4/5/2010 === * Modified '''IFILE''' class methods ''ifread''' & '''readFromFile''' to return an '''int''…')
• 15:39, 2 April 2010 (diff | hist) . . (0)‎ . . LibStatGen: BAM ‎ (→‎SAM/BAM File)
• 15:38, 2 April 2010 (diff | hist) . . (-11)‎ . . LibStatGen: FASTQ ‎
• 15:37, 2 April 2010 (diff | hist) . . (+325)‎ . . LibStatGen: FASTQ ‎
• 15:34, 2 April 2010 (diff | hist) . . (+363)‎ . . FastQValidator ‎
• 09:33, 31 March 2010 (diff | hist) . . (-4)‎ . . LibStatGen: BAM ‎ (→‎SAM/BAM File)
• 09:18, 31 March 2010 (diff | hist) . . (-12)‎ . . C++ Class: SamFile ‎
• 16:26, 29 March 2010 (diff | hist) . . (+962)‎ . . LibStatGen: BAM ‎
• 08:37, 26 March 2010 (diff | hist) . . (+470)‎ . . LibStatGen: BAM ‎
• 16:29, 25 March 2010 (diff | hist) . . (+86)‎ . . LibStatGen: BAM ‎
• 16:19, 25 March 2010 (diff | hist) . . (+31)‎ . . LibStatGen: BAM ‎
• 15:09, 25 March 2010 (diff | hist) . . (+364)‎ . . LibStatGen: BAM ‎
• 14:29, 25 March 2010 (diff | hist) . . (+41)‎ . . FastQValidator ‎
• 14:24, 25 March 2010 (diff | hist) . . (-2)‎ . . FastQValidator ‎ (→‎Status)
• 14:23, 25 March 2010 (diff | hist) . . (+126)‎ . . FastQValidator ‎
• 10:58, 25 March 2010 (diff | hist) . . (+92)‎ . . FastQValidator ‎
• 10:56, 25 March 2010 (diff | hist) . . (+350)‎ . . FastQValidator ‎
• 10:54, 25 March 2010 (diff | hist) . . (+513)‎ . . LibStatGen: FASTQ ‎
• 09:12, 25 March 2010 (diff | hist) . . (+61)‎ . . Main Page ‎
• 16:46, 24 March 2010 (diff | hist) . . (+48)‎ . . LibStatGen: BAM ‎
• 16:41, 24 March 2010 (diff | hist) . . (+4,673)‎ . . LibStatGen: BAM ‎
• 13:09, 23 March 2010 (diff | hist) . . (-1)‎ . . LibStatGen: BAM ‎ (→‎Reading/Writing SAM/BAM Files In Your Program)
• 13:09, 23 March 2010 (diff | hist) . . (+969)‎ . . LibStatGen: BAM ‎
• 14:47, 22 March 2010 (diff | hist) . . (+2)‎ . . SAM Validation Criteria ‎ (→‎BamFile Class)
• 14:47, 22 March 2010 (diff | hist) . . (+34)‎ . . SAM Validation Criteria ‎
• 14:44, 22 March 2010 (diff | hist) . . (+37)‎ . . N BamFile/SAM Validation Criteria ‎ (moved BamFile/SAM Validation Criteria to SAM Validation Criteria over redirect) (current)
• 14:44, 22 March 2010 (diff | hist) . . (0)‎ . . m SAM Validation Criteria ‎ (moved BamFile/SAM Validation Criteria to SAM Validation Criteria over redirect)
• 14:42, 22 March 2010 (diff | hist) . . (0)‎ . . m SAM Validation Criteria ‎ (moved SAM Validation Criteria to BamFile/SAM Validation Criteria)
• 11:23, 19 March 2010 (diff | hist) . . (+160)‎ . . LibStatGen: BAM ‎
• 18:22, 18 March 2010 (diff | hist) . . (+530)‎ . . SAM Validation Criteria ‎
• 12:01, 18 March 2010 (diff | hist) . . (+75)‎ . . SAM Validation Criteria ‎
• 09:47, 18 March 2010 (diff | hist) . . (+9)‎ . . LibStatGen: BAM ‎
• 09:47, 18 March 2010 (diff | hist) . . (+293)‎ . . LibStatGen: BAM ‎ (→‎Setting fields in a SAM/BAM Header)
• 14:52, 17 March 2010 (diff | hist) . . (+1,965)‎ . . SAM Validation Criteria ‎ (→‎SAM Alignment Validation)
• 14:44, 17 March 2010 (diff | hist) . . (+1,638)‎ . . SAM Validation Criteria ‎
• 14:38, 17 March 2010 (diff | hist) . . (+52)‎ . . SAM Validation Criteria ‎
• 14:30, 17 March 2010 (diff | hist) . . (+2,441)‎ . . N SAM Validation Criteria ‎ (Created page with '=== SAM Header Validation Rules === TODO === SAM Alignment Validation === {| class="wikitable" style="width:100%" border="1" |+ style="font-size:150%"|'''SAM Alignment Record'''…')
• 14:29, 17 March 2010 (diff | hist) . . (+73)‎ . . LibStatGen: BAM ‎
• 11:43, 17 March 2010 (diff | hist) . . (+3)‎ . . LibStatGen: BAM ‎ (→‎Read & Write BAM/SAM Executable)
• 11:42, 17 March 2010 (diff | hist) . . (+404)‎ . . LibStatGen: BAM ‎
• 11:38, 17 March 2010 (diff | hist) . . (+426)‎ . . LibStatGen: BAM ‎
• 17:08, 16 March 2010 (diff | hist) . . (+1,656)‎ . . LibStatGen: BAM ‎ (→‎Retrieving fields from a SAM/BAM Record)

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