USeq Source Code

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

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

Improved usage statements.

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.

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

Fixed an issue where only one of the two paired-end bisulfite fastq files was getting split, resulting in only one of the two aligning.

1. Fixed issue where analysis# = null in cmd.txt when multiple samples from the same experiment number listed
2. Fixed an issue where Tomato couldn't find the newly created analysis report to drop in the log.txt file.
3. Fixed error where Tomato couldn't find the appropriate jobs dir for subsamples.
4. Added more sequencing application codes to the list of abbreviated codes
5. Fixed error with moving parsed fresh data report to processedReports folder.
6. Changed code to soft link input fastq files instead of specifying full path (Tomato doesn't allow calling full path)

Updated regex string to match exception cases for genome build as reported by GNomEx

Fixed location of directory for httpclient_create_analysis.sh that calls createAnalysisMain

Fixed index out of bounds bug when input fresh data report is missing expected column.