Substitute htsnexus_test_NA12878 test data with hg38-based alternative #329
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… needs to be swapped) and unmapped reads (those need to be injected into the file(s)?)...
…rnings for our usecase AFAICT: % samtools view -C -T hg38.fa --output-fmt-option version=3.1 -o seraseq_cepba_larger.cram seraseq_cebpa_larger.bam [W::cram_get_ref] Reference file given, but ref 'chrEBV' not present [W::cram_get_ref] Failed to populate reference for id 455 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference
…oduced in both BAM and CRAM files... potentially cleanup the garbage chromosome symbols too (clutter drop down menus on genome viewers, making testing clumsy)
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Motivation: The reference genome build used by htsnexus test files,
hs37d5is problematic with genome viewers since it's not typically available and needs to be custom built, making testing and development harder for third parties.