debugString function added #516
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scripts/test.sh
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| @@ -18,4 +18,4 @@ trap finish EXIT | |||
| sleep 1 | |||
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| # Start the tests | |||
| mocha-phantomjs http://localhost:8081/src/test/runner.html "$@" | |||
| mocha-phantomjs -p /usr/local/bin/phantomjs http://localhost:8081/src/test/runner.html "$@" | |||
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this file should not be modified.
src/test/GA4GHAlignment-test.js
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| @@ -36,6 +36,8 @@ describe('GA4GHAlignment', function() { | |||
| pos: 10007, | |||
| strand: '-' | |||
| }); | |||
| expect(a.debugString().length).to.be.above(0); | |||
| console.log("GA4GHAlignment : " + a.debugString()); | |||
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remove console statement
src/test/data/SamRead-test.js
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| @@ -44,6 +44,8 @@ describe('SamRead', function() { | |||
| pos: 79, | |||
| strand: '-' | |||
| }); | |||
| expect(read.debugString().length).to.be.above(0); | |||
| console.log("SamRead : " + read.debugString()); | |||
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remove console statement
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Fixes #494 |
src/main/GA4GHAlignment.js
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| @@ -118,5 +128,8 @@ class GA4GHAlignment /* implements Alignment */ { | |||
| return alignment.fragmentName + ':' + alignment.readNumber; | |||
| } | |||
| } | |||
| function makeCigarString(cigarOps: Array<CigarOp>) { | |||
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It looks like this function is copied from SamRead.js. Can you move this function to Alignment.js from both SamRead and GA4GHAlignment and reference the function from Alignment.js?
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The function is actually not directly copied from SamRead.js. The function signatures are different in GA4GHAlignment.js and SamRead.js
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It would be great if we could actually change the SamRead function to match yours, considering it enforces types. We can still create a function in Alignment.js and modify the usage in SamRead.js to call the function in Alignment.js
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I made the edits, I think it should work.
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Thanks @abhim00 ! |
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