User contributions for Pha

4 October 2011

• 14:4714:47, 4 October 2011 diff hist +229 BamUtil: convert →BAM File Recovery: better grammar and more text
• 14:4414:44, 4 October 2011 diff hist +1,047 BamUtil: convert add recovery section
• 14:3214:32, 4 October 2011 diff hist +60 m BamUtil: convert →Parameters: add recover option

2 November 2010

• 16:3316:33, 2 November 2010 diff hist +7,682 N QPLOT initial copy from internal wiki - needs more edits

30 July 2010

• 13:4013:40, 30 July 2010 diff hist +64 m SAM →What is SAM: second test
• 13:3813:38, 30 July 2010 diff hist +59 m SAM →What is SAM: test edit - revert
• 13:3013:30, 30 July 2010 diff hist +136 SAM →What is SAM: refer to BamFile c++ library code
• 13:2813:28, 30 July 2010 diff hist +477 BAM elaborate on details

29 July 2010

• 16:3016:30, 29 July 2010 diff hist +257 SAM →What is SAM: simplify and elaborate

16 July 2010

• 13:0613:06, 16 July 2010 diff hist +4 m BamGenotypeCheck fix indenting
• 13:0513:05, 16 July 2010 diff hist +453 BamGenotypeCheck add pointer to fresh karma download

22 June 2010

• 10:5710:57, 22 June 2010 diff hist −2 m BamGenotypeCheck →Input Files: fix link
• 10:5610:56, 22 June 2010 diff hist +60 BamGenotypeCheck →Input Files: add fasta link
• 10:5410:54, 22 June 2010 diff hist +21 BamGenotypeCheck →Input Files: more detail
• 10:5310:53, 22 June 2010 diff hist +81 BamGenotypeCheck →Filtering: add -f option
• 10:4810:48, 22 June 2010 diff hist +1 m Main Page →Sequence Analysis Tools: change name
• 10:4710:47, 22 June 2010 diff hist +4 BamGenotypeCheck rename again
• 10:4610:46, 22 June 2010 diff hist +30 N GenotypeIDcheck moved GenotypeIDcheck to BamGenotypeCheck: a better name was suggested current
• 10:4610:46, 22 June 2010 diff hist 0 m BamGenotypeCheck moved GenotypeIDcheck to BamGenotypeCheck: a better name was suggested

21 June 2010

• 11:1911:19, 21 June 2010 diff hist +18 m Software change layout a little
• 11:0611:06, 21 June 2010 diff hist +488 BamGenotypeCheck total rewrite - new program
• 10:2310:23, 21 June 2010 diff hist −1 m Main Page rename BAMidentity check to genotypeIDcheck to match new program name
• 10:2210:22, 21 June 2010 diff hist +29 N BamIdentityCheck moved BamIdentityCheck to GenotypeIDcheck: now matches the new program name current
• 10:2210:22, 21 June 2010 diff hist 0 m BamGenotypeCheck moved BamIdentityCheck to GenotypeIDcheck: now matches the new program name

8 June 2010

• 09:4909:49, 8 June 2010 diff hist +27 m BAM Review Action Items add new name options, spelling corrections

20 April 2010

• 14:1814:18, 20 April 2010 diff hist +88 Verifying Sample Identities - Implementation →Mathematical Details

13 April 2010

• 16:3716:37, 13 April 2010 diff hist +320 C++ Class: Pedigree Example →Example current
• 16:3516:35, 13 April 2010 diff hist +532 C++ Class: Pedigree Example →Example
• 16:3116:31, 13 April 2010 diff hist +1 C++ Class: Pedigree Example →Example
• 16:3116:31, 13 April 2010 diff hist +1,000 N C++ Class: Pedigree Example Created page with '== Example == <source lang="cpp"> #include "Pedigree.h" int main(int argc, char ** argv); { Pedigree ped; // The data file contains a description of the contents of the…'
• 16:2416:24, 13 April 2010 diff hist +200 Verifying Sample Identities - Implementation →Mathematical Details
• 16:2016:20, 13 April 2010 diff hist +574 Verifying Sample Identities - Implementation →Mathematical Details
• 16:0916:09, 13 April 2010 diff hist +79 Verifying Sample Identities - Implementation →Mathematical Details
• 16:0316:03, 13 April 2010 diff hist +1,786 Verifying Sample Identities - Implementation →Mathematical Details
• 15:5215:52, 13 April 2010 diff hist +233 Verifying Sample Identities - Implementation →Mathematical Details
• 15:4915:49, 13 April 2010 diff hist −8 Verifying Sample Identities - Implementation →Mathematical Details
• 15:4915:49, 13 April 2010 diff hist +78 Verifying Sample Identities - Implementation No edit summary
• 15:4715:47, 13 April 2010 diff hist +1,533 N Verifying Sample Identities - Implementation Created page with '== Principle == We should be able to verify that the right sample has been sequenced by comparing base calls in a read to known genotypes for a sample. If the sample has been s…'

9 April 2010

• 10:3010:30, 9 April 2010 diff hist +402 Karma →Karma CHANGELOG: fill in 0.9.0 changes
• 10:0110:01, 9 April 2010 diff hist +478 Karma add TODO items and begin listing change history

8 April 2010

• 15:2215:22, 8 April 2010 diff hist +372 Karma add features/benefits
• 15:1315:13, 8 April 2010 diff hist +1 Karma →Other useful links
• 15:1315:13, 8 April 2010 diff hist +70 Karma →Karma Performance Tuning
• 15:1115:11, 8 April 2010 diff hist +477 Karma fill in build info
• 15:0515:05, 8 April 2010 diff hist +166 Karma →Dependencies: fill em in
• 15:0315:03, 8 April 2010 diff hist +3,588 Karma fill in performance details
• 14:3614:36, 8 April 2010 diff hist −169 Karma add mapping examples
• 14:2514:25, 8 April 2010 diff hist +930 Karma populate alignment section
• 14:0714:07, 8 April 2010 diff hist +84 m Karma →Testing the build: more detail
• 14:0714:07, 8 April 2010 diff hist +493 Karma →Testing the build: flesh it out