Amalgamate multiple CIGAR ops into single entry.

[whitwham]

Multiple matching (or sequence (mis)matching)) ops (e.g. 10M40M) give a different VCF using BAQ than a single operation of the same length (e.g. 50M). This change compresses the multiple operations into one.

In combination with samtools/bcftools#1914 it should fix #1597.

[whitwham]

Some small corrections, and a suggestion which I can take or leave either way.

It could also do with test data demonstrating the problem, but I can't reproduce it! I'll take a look at the original issue and see if I can get something smaller to test on.

To replicate the original error you also need the version of bcftools without the fix. This change keeps the ID=16 numbers the same, the bcftools one has the alternative bases.

Also, the test data the provided by the users was the smallest they could produce to show the error.

[jkbonfield]

I've managed to produce something really tiny now, starting with the original test data provided. I think that's just simulated data, but I don't know the license on it so will try and figure out the cause of it going wrong to produce our own.

The easiest way I found of reproducing it also, and what we'd need here, is via test/test_realn. We already have test files, so we can just add one more with two entries using =/X vs M.

[jkbonfield]

Here is some test data.

test/realn03.fa

>MX
CGTCTACTACG

test/realn03.sam

@HD VN:1.6  SO:coordinate
@SQ SN:MX   LN:11
M   64  MX  1   60  11M *   0   0   CGTCTCCTACG IIIIIIIIIII
X   64  MX  1   60  5=1X5=  *   0   0   CGTCTCCTACG IIIIIIIIIII

Then run:

./test/test_realn -e -f test/realn03.fa -i test/realn03.sam

You should see the same BQ tag in both cases, but don't with develop. There are already test files for test_realn, so this can just be another 1 to add and put into test.pl

I've verified it's only affecting extended mode, which tallies with the code changes.