merge from devel to create release 65.0 #532
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merge master patches to devel
…filter.stats for easier identificaton
trim tag metrics in viewer
add genotype_call_results_reporter script
upstream_tags check: standardise access to the tracking database
Make use of recent bwa (typ. > 0.7) explicit with bwa0_6 in checks
change naming of spatial_filter stats files for spatial_filter check
Removed C utilities, replaced from Conda channel.
Removed C utilities, replaced from Conda channel
…er.jar; use standard samtools command accessor
autoqc checks - remove dependency on tracking XML
use WTSI::DNAP::Utilities::Build as a base
remove vestiges of decoding with BamIndexDecoder.jar
remove unused functionality in Build.PL
adapter check - remove code that used fastq files as input
autoqc check execute method to error if input files do not exist
use default bcftools executable
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