User contributions for Goncalo

29 January 2014

• 09:5109:51, 29 January 2014 diff hist −7 Minimac →using a VCF reference panel
• 08:4608:46, 29 January 2014 diff hist +541 Tutorial: RAREMETAL No edit summary

16 January 2014

• 18:1918:19, 16 January 2014 diff hist +21 Abecasis Lab →Graduate Students

16 December 2013

• 11:3811:38, 16 December 2013 diff hist +13 Abecasis Lab →Former Masters Students
• 11:3711:37, 16 December 2013 diff hist −1 Abecasis Lab →Graduate Students

6 December 2013

• 16:0816:08, 6 December 2013 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
• 16:0816:08, 6 December 2013 diff hist +83 Biostatistics 830: Main Page →Class Worksheets
• 16:0816:08, 6 December 2013 diff hist 0 N File:Question Sheet - Jun et al (2012) American Journal of Human Genetics.pdf No edit summary current

4 December 2013

• 16:0716:07, 4 December 2013 diff hist 0 Rvtests →Genotyep filters
• 15:4415:44, 4 December 2013 diff hist +1 RAREMETAL Documentation →Where to Download
• 13:3013:30, 4 December 2013 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
• 13:3013:30, 4 December 2013 diff hist +82 Biostatistics 830: Main Page →Class Worksheets
• 13:2913:29, 4 December 2013 diff hist 0 N File:Question Sheet - Wu et al (2011) American Journal of Human Genetics.pdf No edit summary current

26 November 2013

• 18:0318:03, 26 November 2013 diff hist +64 Biostatistics 830: Main Page →Class Worksheets
• 17:5517:55, 26 November 2013 diff hist 0 N File:Question Sheet - Liu et al (2013) Nature Genetics.pdf No edit summary

25 November 2013

• 16:3316:33, 25 November 2013 diff hist 0 Biostatistics 830: Main Page →Class Worksheets
• 16:3316:33, 25 November 2013 diff hist +93 Biostatistics 830: Main Page →Class Worksheets
• 16:1016:10, 25 November 2013 diff hist +94 Biostatistics 830: Main Page →Class Worksheets
• 16:0116:01, 25 November 2013 diff hist 0 N File:Question Sheet - Li and Durbin (2011) Nature.pdf No edit summary current

18 November 2013

• 18:1918:19, 18 November 2013 diff hist +28 Abecasis Group Awards No edit summary
• 18:1918:19, 18 November 2013 diff hist +152 Abecasis Group Awards →International Genetic Epidemiology Society

12 November 2013

• 16:1016:10, 12 November 2013 diff hist −1 Biostatistics 830: Main Page →Class Worksheets
• 16:0916:09, 12 November 2013 diff hist +7 Biostatistics 830: Main Page →Class Worksheets
• 16:0916:09, 12 November 2013 diff hist +60 Biostatistics 830: Main Page →Class Worksheets
• 16:0916:09, 12 November 2013 diff hist 0 N File:Question Sheet - Iqbal et al (2012) Nature Genetics.pdf No edit summary

7 November 2013

• 04:0104:01, 7 November 2013 diff hist +146 Biostatistics 830: Main Page →Class Worksheets
• 04:0004:00, 7 November 2013 diff hist 0 File:Question Sheet - Zerbino and Birney (2008) Bioinformatics.pdf Goncalo uploaded a new version of "File:Question Sheet - Zerbino and Birney (2008) Bioinformatics.pdf": Removed unnecessary second page. current
• 03:5803:58, 7 November 2013 diff hist 0 File:Question Sheet - Li and Durbin (2009) Bioinformatics.pdf Goncalo uploaded a new version of "File:Question Sheet - Li and Durbin (2009) Bioinformatics.pdf": Fixed typos in code example. current
• 03:5703:57, 7 November 2013 diff hist 0 N File:Question Sheet - Zerbino and Birney (2008) Bioinformatics.pdf No edit summary

30 October 2013

• 12:1912:19, 30 October 2013 diff hist +78 Biostatistics 830: Main Page →Class Worksheets
• 12:1912:19, 30 October 2013 diff hist 0 N File:Question Sheet - Li and Durbin (2009) Bioinformatics.pdf No edit summary
• 12:1812:18, 30 October 2013 diff hist +24 Biostatistics 830: Main Page →Class Worksheets

28 October 2013

• 16:0916:09, 28 October 2013 diff hist +6 830 - MaqIndex::LookupWord() No edit summary current
• 13:5813:58, 28 October 2013 diff hist +268 N 830 - BestAlignment::IterateCache() Created page with "<source lang="cpp"> unsigned int BestAlignment::IterateCache(unsigned int key) { int h = (key * PRIME) % cacheSize; while (cache[h] != -1 && cache[h] ..." current
• 13:5313:53, 28 October 2013 diff hist +4 Biostatistics 830 - Code Snippets →Code Snippets current
• 13:5313:53, 28 October 2013 diff hist +51 N 830 - BestAlignment::ClearCache() Goncalo moved page 830 - BestAlignment::ClearCache() to 830 - BestAlignment::ClearPositions() current
• 13:5313:53, 28 October 2013 diff hist 0 m 830 - BestAlignment::ClearPositions() Goncalo moved page 830 - BestAlignment::ClearCache() to 830 - BestAlignment::ClearPositions() current
• 13:5213:52, 28 October 2013 diff hist +142 N 830 - BestAlignment::ClearPositions() Created page with "<source lang="cpp"> void BestAlignment::ClearPositions() { cacheItems = 0; for (int i = 0; i < cacheSize; i++) cache[i] = -1; } </source>"
• 13:5113:51, 28 October 2013 diff hist +265 N 830 - BestAlignment::isNewPosition() Created page with "<source lang="cpp"> bool BestAlignment::isNewPosition(unsigned int pos) { int h = IterateCache(pos); if (cache[h] == pos) return false; cache[h] = pos; cacheItems++; ..." current
• 13:4913:49, 28 October 2013 diff hist +122 Biostatistics 830 - Code Snippets →Code Snippets
• 13:4713:47, 28 October 2013 diff hist +32 830 - BestAlignment::EvaluateAlignment() (detailed comparison) No edit summary current
• 13:4713:47, 28 October 2013 diff hist +584 N 830 - BestAlignment::EvaluateAlignment() (detailed comparison) Created page with "void BestAlignment::EvaluateAlignment(String & reference, FastQ & read, unsigned int pos, bool fwd) { if (pos < 0 || read.Length() + pos > reference.Length()) return; if ..."
• 13:4613:46, 28 October 2013 diff hist +350 N 830 - BestAlignment::EvaluateAlignment() (main loop) Created page with "<source lang="cpp"> void BestAlignment::EvaluateAlignment(MaqIndex & index, FastQ & read, unsigned int offset, bool fwd) { unsigned int start, stop; index.LookupWord(read...." current
• 13:4513:45, 28 October 2013 diff hist +32 830 - BestAlignment::MaqAlignment() No edit summary current
• 13:4413:44, 28 October 2013 diff hist +1,224 N 830 - BestAlignment::MaqAlignment() Created page with "void BestAlignment::MaqAlignment(MaqIndex & index1, MaqIndex & index2, MaqIndex & index3, FastQ & read) { position = -1; sumQ = mapQ = 0; mismatches = read.Length(); forwa..."
• 13:4413:44, 28 October 2013 diff hist +167 Biostatistics 830 - Code Snippets →Code Snippets
• 13:3913:39, 28 October 2013 diff hist +500 N 830 - MaqIndex::GetWord() Created page with "<source lang="cpp"> long long MaqIndex::GetWord(String & sequence, unsigned int position) { long long word = 0; if (position + mask.Length() > sequence.Length()) return -..." current
• 13:3813:38, 28 October 2013 diff hist +613 N 830 - MaqIndex::BuildIndex() Created page with "<source lang="cpp"> void MaqIndex::BuildIndex() { // This function could use quite a lot of memory ... // 4 bytes per word // 4 bytes per position // 4 bytes per ..." current
• 13:3613:36, 28 October 2013 diff hist +1,079 N 830 - MaqIndex::LookupWord() Created page with "<source lang="cpp"> bool MaqIndex::LookupWord(String & sequence, int offset, unsigned int & firstOccurrence, unsigned int & lastOccurrence) { firstOccurrence = 0; lastOccurr..."
• 13:3413:34, 28 October 2013 diff hist −2 830 - MaqIndex::CompareToIndex() No edit summary current