added getCigar method to record

[wilsonGen]

added getCigar method to CramRecord,

for example :
record.getCigar() // "50S100M"

[cmdcolin]

nice work! it may be worth adding some testing to make sure this matches samtools decoding. we have our own "read features to cigar string" in jbrowse that uses code created by @jkbonfield that has some corner case handling that i'm not sure actually come up in practice(?)

code here https://github.com/GMOD/jbrowse-components/blob/main/plugins/alignments/src/CramAdapter/util.ts#L132-L251

[wilsonGen]

thank you for reviewing!
Sorry, actually this is the first time I create a pull request, how should I add the testing?

[cmdcolin]

in the absense of 'synthesizing' read features from thin air, one way to test is to use samtools on a small test file (we have some test files in test/data/ folder) to create a list of CIGAR strings, and then run cram-js to generate CIGAR strings on the same file, and check that they match up

[cmdcolin]

just wanted to check back to see if you were interested in adding tests for this?

[wilsonGen]

Yes, I am interested, sorry for holding it so long.
Just want to ask, should I create a test script or should I just run it and compare the results myself?

[rbuels]

Please add automated test code similar to the tests that are already in the repository. Run `npm test` or `yarn test` to run the tests and see their results.

…

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[wilsonGen]

Thank you! I will try to add the test next week!

[wilsonGen]

Just improved the getCigar() so that it handles hard clip as well,
also added automated test code for getCigar(), to make sure it matches the cigar from samtools.
Thank you all for reviewing my code and suggesting ways to ensure correct result, I have learnt a lot!