fixed an error where the read mate key in SplitNCigarReads was not sufficiently strict about readnames causing cigar errors #6909
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Travis reported job failures from build 31916
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lbergelson
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Oct 29, 2020
.travis.yml
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| @@ -110,14 +110,14 @@ install: | |||
| elif [[ $TEST_DOCKER == true ]]; then | |||
| echo "Skip the install because we're doing a docker build"; | |||
| else | |||
| ./gradlew assemble; | |||
| ./gradlew installDist; | |||
| sudo ./gradlew assemble; | |||
| @VisibleForTesting | ||
| static String makeKey(String name, boolean firstOfPair, int mateStart) { | ||
| // NOTE: We use the '@' character here because it is explicitly forbidden for use in read names by the SAM Spec and we don't want to risk accidental matches across read pairs | ||
| return name + "@" + (firstOfPair ? 1 : 0) + "@" + mateStart; |
| @@ -201,6 +201,20 @@ public void testMappingReadMateRepair() { | |||
| Assert.assertEquals(read2.getMateStart(), 10003); | |||
| } | |||
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| @Test | |||
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@jamesemery Have you tested what happens if you add a read with a @s in the name which could recreate the problem?
lbergelson
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Oct 29, 2020
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Travis reported job failures from build 32069
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…fficiently strict about readnames causing cigar errors
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Fixes #6776