/** * default signature that forces the lists to be the same size * * @param s1 a list of sequence headers * @param s2 a second list of sequence headers */ public static void assertSequenceListsEqual(final List<SAMSequenceRecord> s1, final List<SAMSequenceRecord> s2) { assertSequenceListsEqual(s1, s2, false); } /**
/** * default signature that forces the lists to be the same size * * @param s1 a list of sequence headers * @param s2 a second list of sequence headers */ public static void assertSequenceListsEqual(final List<SAMSequenceRecord> s1, final List<SAMSequenceRecord> s2) { assertSequenceListsEqual(s1, s2, false); } /**
/** * Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only). * * @param s1 a list of sequence headers * @param s2 a second list of sequence headers * @param checkPrefixOnly a flag specifying whether to only look at the first records in the lists. This will then check that the * records of the smaller dictionary are equal to the records of the beginning of the larger dictionary, which can be useful since * sometimes different pipelines choose to use only the first contigs of a standard reference. */ public static void assertSequenceDictionariesEqual(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2, final boolean checkPrefixOnly) { if (s1 == null || s2 == null) return; assertSequenceListsEqual(s1.getSequences(), s2.getSequences(), checkPrefixOnly); }
/** * Throws an exception if both parameters are non-null and unequal. */ public static void assertSequenceDictionariesEqual(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2) { if (s1 == null || s2 == null) return; assertSequenceListsEqual(s1.getSequences(), s2.getSequences()); }
/** * Returns true if both parameters are null or equal, otherwise returns false */ public static boolean areSequenceDictionariesEqual(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2) { if (s1 == null && s2 == null) return true; if (s1 == null || s2 == null) return false; try { assertSequenceListsEqual(s1.getSequences(), s2.getSequences()); return true; } catch (SequenceListsDifferException e) { return false; } }
/** * Throws an exception if both (first) parameters are non-null and unequal (if checkPrefixOnly, checks prefix of lists only). * * @param s1 a list of sequence headers * @param s2 a second list of sequence headers * @param checkPrefixOnly a flag specifying whether to only look at the first records in the lists. This will then check that the * records of the smaller dictionary are equal to the records of the beginning of the larger dictionary, which can be useful since * sometimes different pipelines choose to use only the first contigs of a standard reference. */ public static void assertSequenceDictionariesEqual(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2, final boolean checkPrefixOnly) { if (s1 == null || s2 == null) return; assertSequenceListsEqual(s1.getSequences(), s2.getSequences(), checkPrefixOnly); }
/** * Returns true if both parameters are null or equal, otherwise returns false * * @param s1 a list of sequence headers * @param s2 a second list of sequence headers */ public static boolean areSequenceDictionariesEqual(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2) { if (s1 == null && s2 == null) return true; if (s1 == null || s2 == null) return false; try { assertSequenceListsEqual(s1.getSequences(), s2.getSequences()); return true; } catch (final SequenceListsDifferException e) { return false; } }
/** * Returns true if both parameters are null or equal, otherwise returns false * * @param s1 a list of sequence headers * @param s2 a second list of sequence headers */ public static boolean areSequenceDictionariesEqual(final SAMSequenceDictionary s1, final SAMSequenceDictionary s2) { if (s1 == null && s2 == null) return true; if (s1 == null || s2 == null) return false; try { assertSequenceListsEqual(s1.getSequences(), s2.getSequences()); return true; } catch (final SequenceListsDifferException e) { return false; } }