0.39.0

• use "samtools index" instead of "cram_index to create cram indexes
• for bam and cram index creation, use "samtools index -o <index_file>" to explicitly indicate the index file

0.38.0

• add additional autosome specific coverage threshold to final_output_prep.json

0.37.2

• change bambi i2b command in stage1 analysis to use new boolean version of --nocall-quality flag

0.37.1

• amend markdup command chain for duplexseq (nanoseq) analyses
• updated to use samtools merge instead of bammerge for library merging

0.37.0

• add i2b_nocall_qual_switch to stage1 analysis to enable "--nocall-quality=2" to be set for bambi i2b

0.36.0

• add hs_bwa_executable parameter to allow different bwa executables for target and nchs alignments (e.g. bwa-mem2 and bwa0_6)
• add optminpixeldif flag (optical distance for duplicates) to bamstreamingmarkduplicates command (biobambam markdup method)

0.35.0

replace scramble with samtools in analysis pipeline templates

0.34.0

• add calmd to biobambam,samtools and duplexseq markdup methods

0.33.1

• update CI and tests

0.33.0

• extend list of preserved auxtags in realignment bamreset (for Duplex-Seq)