There seem to be several bugs related to formatting of SAM output @UBrau identified. These are a direct result of a lack of tests for SAM format in tests/runtests.jl which is clearly necessary.
'+' strand introns may be off-by-one, such that downstream of splice junctions is shifted by 1 in igv browser.
Genes on minus strand may be placed in mirror image coordinates.
Some CIGAR strings are wrong based on one-sided soft-padding.
There seem to be several bugs related to formatting of SAM output @UBrau identified. These are a direct result of a lack of tests for SAM format in
tests/runtests.jl
which is clearly necessary.