0.9.13

fixes for nonconsented human split with no target alignment

• change intermediate OUTFILE node to RAFILE
• remove unneeded bammarkduplicates and parameters only used by sort and duplicate marking

0.19.2

0.19.2

0.19.1

ysplit fix

0.19.0

• add new templates for STAR alignment and Salmon
• Small change in final_output_prep to allow bamsort_cmd to have configurable executable and scramble to have optional embed reference param.
• add select directive
• splice/prune operations can be specified in param_vals file
• new version2 format of port specification in templates
• correct failure to report errors lower than one VTFILE level

0.18.6

Y-split fixes
When processing VTFILE nodes, make sure that parameters are reevaluated locally
use bambi for split by chromosome (remove java)
add tests for VTFILE functionality

0.18.5

• Correct logic in vftp.pl for allowing edges without id attributes
• Reduce verbosity in vtfp.pl
• Fix handling of splice/prune in vftp.pl where source/destination is STDIN/STOUT
• Use fopid in place of other substitutions
• use FindBin in vtfp.pl and viv.pl

0.18.4

release 0.18.4

• removal of -n 1 flag with seqchksum_merge.pl command in merge_aligned template
• logging changes
  correct unneeded warnings about changing use_STDIN/use_STDOUT values for INFILE/OUTFILE/RAFILE node
  recognise JSON::PP:Boolean type (remove warning from log)
  allow edges to have no id values (warnings about undefined values in log files should no longer appear)
• cope with differing line return behaviour of versions of rev utility (test fix)

release 0.18.3

release 0.18.3

• bwa mem flags default changes and additions
  don't use -T by default
  [new flag] use -K 100000000 (reads per thread, large value to make alignment runs replicable)
  [new flag] use -Y to soft clip supplementary alignments instead of hard clipping
• add ability to splice and prune nodes from the final graph
• final_output_prep changes to support optional targeted stats files.
• use threaded bamsormadup in place of bamsort for coord sort
• add parameters to allow selection of java or bambi (default) implementations of i2b and decode

release 0.18.2

release 0.18.2

• propagate any 'AH' fields provided by the aligner when providing full SQ headers (bwa0.7.15)
• fix bamindexdecoder.json template: add pack option to bamindexdecoder_java_cmd array to handle undefined parameters; change default implementation from "samtools decode" back to java BamIndexDecoder

patch release 0.18.1

corrected mistyped attribute name additem which could casue compilation errors