v2.1.15

Accept .tsv as a possible line ending for custom samplesheets in illumina demux [#47]

v2.1.14

• adds --max_barcodes option (default 10000) to cap common barcodes output file length from illumina.illumina_demux [#46]

v2.1.13

• bugfixes for file_utils.tsv_join -- make it behave more unix-like instead of excel-like [#45]

v2.1.12

• viral-baseimage 0.1.18 -> 0.1.19 (#44)

v2.1.11

• JVMmemory is now passed to additional picard tools in read_utils.py align_and_fix

v2.1.10

• bump viral-baseimage 0.1.17 -> 0.1.18 (includes faster miniconda and mamba)
• use bioconda-sourced GATKv3

v2.1.9

• Adjust output filter of read_utils.align_and_fix() to remove marked pcr duplicates, mapped singletons, supplementary (chimeric) alignments, secondary alignments, and improperly paired reads. single-end reads are allowed through if mapped.

v2.1.8

Addition of a few scripts: tsv_join, tsv_derived_cols, and priorities.py [#37]

v2.1.7

• bugfix for read_utils.py align_and_fix when empty input and aligner = minimap2 [#36]

v2.1.6

• bugfix: minimap2 behavior when given empty bam input with exactly one read group [#35]