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Replace open_or_gzopen() with smart_open() from external library

Status: Open.

#116 In broadinstitute/viral-core;

· tomkinsc opened on Dec 12, 2024

inference of sequencer model needs updating

Status: Open.

#108 In broadinstitute/viral-core;

· dpark01 opened on Aug 3, 2024

Replace custom custom mode selection in zstd_open() with zstandard.open()

Status: Open.

#105 In broadinstitute/viral-core;

· tomkinsc opened on Jul 16, 2024

Fail gracefully on bam with no reads in viral-core::read_utils::minimap2_idxstats(), and/or provide informative error message

Status: Open.

#101 In broadinstitute/viral-core;

· tomkinsc opened on Apr 25, 2024

update conda python version

Status: Open.

#96 In broadinstitute/viral-core;

· dpark01 opened on Mar 11, 2024

Preserve read pairing information in FastqToSamTool when provided single fastq with interleaved reads

Status: Open.

#83 In broadinstitute/viral-core;

· tomkinsc opened on Aug 10, 2023

Eliminate ExtractIlluminaBarcodes call by default prior to IlluminaBaseCallsToSam

Status: Open.

#82 In broadinstitute/viral-core;

· tomkinsc opened on Apr 19, 2023

Handle more date formats from RunInfo.xml

Status: Open.

#79 In broadinstitute/viral-core;

· dpark01 opened on Dec 13, 2022

implement a new bam filtration step

Status: Open.

#22 In broadinstitute/viral-core;

· dpark01 opened on May 14, 2020

tools.bwa.filter_sam_on_alignment_score is a memory hog

Status: Open.

#21 In broadinstitute/viral-core;

· dpark01 opened on May 7, 2020