USeq / Source Code Commit Log

Commit	Date
[r68] by biotelerock Fixed the wording of the help menu.	2013-02-27 22:23:48	Tree
[r67] by biotelerock Added changes for 5.8.1	2013-02-20 21:52:28	Tree
[r66] by biotelerock Lots of mods: MergePairedSamAlignments * Fixed bug when merging bam files where double line returns where causing Picard's SortSam to error out. VCFTabix * New app for recursing through directories and tabix indexing vcf files USeq2UCSCBig and UCSCBig2USeq * Added new options for skipping for forcing overwrite of already converted files * Added options to silence all but error messages CalculatePerCycleErrorRate * Added ability to work with unsorted sam files * Added option to require read names start with a given prefix. Novoalign is adding in some junk reads to their output? MergeUCSCGeneTable * Fixed bug where 1bp terminal exons were being skipped causing the conversion of bed12 useq files to bb to throw an error. SamTranscriptomeParser * Fixed bug where insertions or deletions that occurred at the splice junction were causing the failure to insert an appropriate number of Ns	2013-02-20 21:51:57	Tree
[r65] by biotelerock Added InosinePredict to build for the Bass lab	2013-02-20 21:48:59	Tree
[r64] by tmosbruger DRSS reports maximum coverage position when run on a single dataset.	2013-02-19 19:17:36	Tree
[r63] by monkeymanstan 1. Fixed bug with matching entire output string from create_analysis_main for new analysis report dir path	2013-02-19 18:28:50	Tree
[r62] by monkeymanstan 1. Added code to parse out versioned genome and store in Sample object field 2. Alignments run through SamTranscriptomeParser after alignment 2. Added flag to reverse strand in STP if paired-end && sequencingApplicationCode = APP2/APP3 3. Added functionality to run all input fastq files through fastqc prior to aligning 4. Added code to create relative read coverage tracks using the Sam2USeq app 5. Added code to run genomic alignments through CalculatePerCycleErrorRate 6. Fixed bug where new Analysis Report dir was not created	2013-02-19 17:04:12	Tree
[r61] by tmosbruger Improved usage statements.	2013-02-19 16:15:34	Tree
[r60] by tmosbruger Added support for counting reads on the reverse strand (native to current illumina pipeline). Also added the ability to count second reads that are either native/flipped. The SamTranscriptomeParser does not flip the strand orientation of the second read by default, so the default settings of the RNASeq and DRDS assume the strand is NOT flipped (native sam). RNASeq and DRDS will run unstranded analysis by default.	2013-02-19 15:40:30	Tree
[r59] by tmosbruger Fixed bug where USeq2Text failed to report isolated scores in the last chromosome.	2013-02-15 21:02:54	Tree

[r68] by biotelerock

Fixed the wording of the help menu.

2013-02-27 22:23:48

Tree

[r67] by biotelerock

Added changes for 5.8.1

2013-02-20 21:52:28

Tree

[r66] by biotelerock

Lots of mods:
MergePairedSamAlignments
* Fixed bug when merging bam files where double line returns where causing Picard's SortSam to error out.
VCFTabix
* New app for recursing through directories and tabix indexing vcf files
USeq2UCSCBig and UCSCBig2USeq
* Added new options for skipping for forcing overwrite of already converted files
* Added options to silence all but error messages
CalculatePerCycleErrorRate
* Added ability to work with unsorted sam files
* Added option to require read names start with a given prefix. Novoalign is adding in some junk reads to their output?
MergeUCSCGeneTable
* Fixed bug where 1bp terminal exons were being skipped causing the conversion of bed12 useq files to bb to throw an error.
SamTranscriptomeParser
* Fixed bug where insertions or deletions that occurred at the splice junction were causing the failure to insert an appropriate number of Ns

2013-02-20 21:51:57

Tree

[r65] by biotelerock

Added InosinePredict to build for the Bass lab

2013-02-20 21:48:59

Tree

[r64] by tmosbruger

DRSS reports maximum coverage position when run on a single dataset.

2013-02-19 19:17:36

Tree

[r63] by monkeymanstan

1. Fixed bug with matching entire output string from create_analysis_main for new analysis report dir path

2013-02-19 18:28:50

Tree

[r62] by monkeymanstan

1. Added code to parse out versioned genome and store in Sample object field
2. Alignments run through SamTranscriptomeParser after alignment
2. Added flag to reverse strand in STP if paired-end && sequencingApplicationCode = APP2/APP3
3. Added functionality to run all input fastq files through fastqc prior to aligning
4. Added code to create relative read coverage tracks using the Sam2USeq app
5. Added code to run genomic alignments through CalculatePerCycleErrorRate
6. Fixed bug where new Analysis Report dir was not created

2013-02-19 17:04:12

Tree

[r61] by tmosbruger

Improved usage statements.

2013-02-19 16:15:34

Tree

[r60] by tmosbruger

Added support for counting reads on the reverse strand (native to current illumina pipeline). Also added the ability to count second reads that are either native/flipped. The SamTranscriptomeParser does not flip the strand orientation of the second read by default, so the default settings of the RNASeq and DRDS assume the strand is NOT flipped (native sam). RNASeq and DRDS will run unstranded analysis by default.

2013-02-19 15:40:30

Tree

[r59] by tmosbruger

Fixed bug where USeq2Text failed to report isolated scores in the last chromosome.

2013-02-15 21:02:54

Tree

USeq Source Code

Source Code Commit Log