Bowtie Code

Redirect fastq-dump's stdout to /dev/null; avoids confusion when it prints status message. Fix parentheses on open() statements. Use fileparse() instead of `basename`.

Use svn instead of cvs to get soapsnp

uint32_t -> ubit32_t since stdint.h is not included

Removed sra file handling function that wasn't ready for primetime. Fixed parens for calls to perl's open function.

Preparing to fix issues with conversion of paired-end SRA files.

Moved def'n of $pre to be at the top.

Fixed issue whereby SRATOOLKIT_HOME was used instead of (tool name)_SRATOOLKIT_HOME. Changed tool-name handling so that name equals to contents of the $TOOL_BASE/TOOLNAME file.

Fixed some open || die's to use parens properly

Corrected the same error in Assign.pl