Final maintenance release for NASP v1

• fix failed coverage/proportion percent columns in sample stats
• fix buffer overflow when exporting long line matrices
• fix "Argument list too long” error when using pre-aligned BAM files
• update defaults for aligners and SNP callers, remove(hide) SolSNP support

v1.0.1

• Support bams with missing ReadGroup header
• Support SNAP aligner v1.0 beta release
• Support picard-tools v1.124+
• Support trimmomatic adapter and quality trimming
• Support tab-autocomplete in command-line interface with the Python readline module
• Improved matrix generation performance
• ...

Known issues:

• Does not support samtools >= 1.3

NASP 0.9.6 - Full Python

NASP Release Notes

0.9.6:

• VCF files with missing headers now throw a "MalformedInputFile" error instead of hanging.
• Rewrote multithreading parameter passing algorithm to fix race condition again.
• Modified data storage algorithm to speed the matrix-building process at the cost of memory use.
• Improvements made to sample and analysis statistics, and new improved statistics file format.
• Aligner and SNP caller program name expected values are now more tolerant and open-ended.
• Insertion data no longer appears in the filtered matrix; one character per matrix cell.
• Files that fail to be read are now represented with blank matrix columns to alert the user.
• Fully Python job dispatcher and command-line UI -- all code now written in Python
• Run log is written to output folder with choices the user made in the UI and commands that were submitted to job manager
• Main nasp executable can accept an XML file with configuration parameters instead of going through UI
• XML configuration file is written to output folder on every run
• Support for SLURM job manager and specifying queues/partitions and other job manager options for both PBS and SLURM