Test secondary alignments #365
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Otherwise (when the field is left empty), samtools view converts it to "*" in the output, which makes testing harder because of spurious differences.
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An improvement I plan to make for #364 affects the code that outputs the secondary alignments. We didn’t have tests covering that, so this adds a couple.
There’s also a change in here related to how empty reads are encoded in SAM output.
samtoolsinsists it should be*, so this is changed here as well.