5.1.0 - full collate and samtools markdup

keiranmraine released this 20 Jun 10:17

· 90 commits to develop since this release

5.1.0

Base image updated to Focal (Ubuntu 20.04).
Majority of biobambam2 replaced with samtools functions.
Reads undergo full collate when mapping from BAM/CRAM (bwa-mem2 prep).
Duplicate marking samtools markdup --mode options exposed to bwa_mem.pl.
- Lanes mapped with earlier versions of PCAP-core cannot be merged without reporocessing to add "mate score tag" via samtools fixmate.
Scramble option for bwa_mem.pl deprecated, relevant option for fast CRAM random access exposed.

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