User contributions
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Jump to navigationJump to search- 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