fix: pretty print with suffix xclip or yclip

[dcroote]

Closes #47.

Thanks @kwuiee, what you identified definitely looks like a bug to me. When running your test:

    fn test_pretty_suffix_xclip_or_yclip() {
        let alignment = Alignment {
            score: -7,
            ystart: 1,
            xstart: 0,
            yend: 4,
            xend: 3,
            ylen: 4,
            xlen: 4,
            operations: vec![Yclip(1), Match, Match, Match, Xclip(1)],
            mode: AlignmentMode::Custom,
        };
        let pretty = concat!(" TCGC\n ||| \nATCG \n\n\n");
        assert_eq!(alignment.pretty(b"TCGC", b"ATCG", 100), pretty);
    }

on the existing code it fails, producing the following output:

running 1 test
thread 'alignment::tests::test_pretty_suffix_xclip_or_yclip' panicked at 'assertion failed: `(left == right)`
  left: `" TCGT\n ||| \nATCG \n\n\n"`,
 right: `" TCGC\n ||| \nATCG \n\n\n"`', src/alignment.rs:557:9

Clearly there is a bug because the left sequence is wrong (terminal T where it should be C).

I've incorporated your test and fix in this PR.

[coveralls]

Pull Request Test Coverage Report for Build 5550351717

• 2 of 2 (100.0%) changed or added relevant lines in 1 file are covered.
• 5 unchanged lines in 4 files lost coverage.
• Overall coverage increased (+0.06%) to 63.539%

---

Files with Coverage Reduction	New Missed Lines	%
src/annot/contig.rs	1	55.75%
src/annot/pos.rs	1	51.43%
src/annot/spliced.rs	1	68.6%
src/genome.rs	2	0%

Totals
Change from base Build 5529481215:	0.06%
Covered Lines:	474
Relevant Lines:	746

---

💛 - Coveralls

[dlaehnemann]

Are you sure this doesn't break non-Custom Alignments? Or maybe to be clearer, is there either (i) a test case that also covers this for for some non-custom Alignment? I could imagine, that the special casing further up is the actual problem? But you dug into this code in more detail, so are probably more confident in answering those question.

[dlaehnemann]

@dcroote Will you have time to have another look here? Otherwise I would probably move ahead with release 1.0.1 at #62 for now...

[dcroote]

Sorry for the delay- I'll need more time to flesh out the test cases so feel free to move ahead with the release

[dlaehnemann]

Just a quick ping to see if there is any planned activity, here. If so, feel free to update the branch, first.