v1.8.2 - bugfix

Minor correction to prevent rerun of markduplicate step if bam_stats fails. More to catch development errors that general use.

v1.8.1 - correct bam_stats calls

Migration from bam_stats.pl to bam_stats (perl to C) introduced a bug.

gnos_pull.pl now allows parallel streams, cleanup of child processes can be unpredictable as the gtdownload client doesn't seem to acknowledge that the parent has shutdown sometimes.

v1.7.1 - Recommended for uses of bwa_mem.pl

BWA mem still produces pairs marked as proper-pairs that are clearly not. This release adds the 'fixmates' option to the sorting step to clean this up.

Also upgrades biobambam to 0.0.191 for convinience of anyone using this as install route.

v1.7.0 - bam_to_sra_sub.pl robustness

Updated to reject any files with non-lowercase UUIDs

Also switched bwa_mem.pl to use C version of bam_stats

v1.6.2 - small bug in setup.sh

Resolved #74

v1.6.1 - Improved resilience to GNOS issues in gnos_pull.pl

• Extend GNOS download commands to accept user specified timeout (see examples/gnos_pull.ini file).
• Catch timeout, warn of occurrence and move onto next download rather than hang indefinitely.
• Add code to prevent multiple instances running against the same output location
  • Makes it easy to setup crons to pull new data as it becomes available.

V1.6.0 - tools for downloading subsets of data

• Adding local file mode for sites that cannot download from GNOS when the xml_to_bas.pl script runs
• gnos_pull.pl - see linked docs

v1.5.4 - bugfix to bam_stats c

bam_stats C no longer requires reference file as a parameter. A warning is in help, and emitted if a cram file is provided with no reference.
Should htslib not find the reference from the cram header and no reference is provided this code may fail.

v1.5.3 - increased robustness of bam_stats C

Changed array for khash in insert size calculations in order to make code more robust.
Header RG line reading now reads anything not a tab or newline as it should when determining what the values of tags are.

v1.5.2 - bamToBw.pl fixes

1. Pull actual binaries from jkent_util not html page associated
2. process name corrections in bamToBw.pm command line args