- implementing the spec change in #1238
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Codecov Report
@@ Coverage Diff @@
## master #1238 +/- ##
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+ Coverage 69.323% 69.676% +0.353%
- Complexity 8105 8321 +216
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Files 543 547 +4
Lines 32480 33069 +589
Branches 5501 5685 +184
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+ Hits 22516 23041 +525
- Misses 7755 7803 +48
- Partials 2209 2225 +16
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| * to mean "same reference as RNAME field." | ||
| */ | ||
| public static final String RESERVED_MRNM_SEQUENCE_NAME = "="; | ||
| public static final String RESERVED_RNEXT_SEQUENCE_NAME = "="; |
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deprecate this instead of just renaming it
| @@ -70,10 +70,12 @@ | |||
| SPECIES_TAG)); | |||
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| // Split on any whitespace | |||
| private static final Pattern SEQUENCE_NAME_SPLITTER = Pattern.compile("\\s"); | |||
| private static final Pattern SEQUENCE_NAME_SPLITTER = Pattern.compile("[\\s]"); | |||
| // These are the chars matched by \\s. | ||
| private static final char[] WHITESPACE_CHARS = {' ', '\t', '\n', '\013', '\f', '\r'}; // \013 is vertical tab | ||
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| private static Pattern LEGAL_RNAME_PATTERN = Pattern.compile("[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*"); |
| @@ -85,8 +87,8 @@ public SAMSequenceRecord(final String name) { | |||
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| public SAMSequenceRecord(final String name, final int sequenceLength) { | |||
| if (name != null) { | |||
| if (SEQUENCE_NAME_SPLITTER.matcher(name).find()) { | |||
| throw new SAMException("Sequence name contains invalid character: " + name); | |||
| if (!LEGAL_RNAME_PATTERN.matcher(name).useAnchoringBounds(true).matches()) { | |||
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move this into the validate method
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SEQUENCE_NAME_SPLITTER in both code and comments can be removed correct? I still see it elsewhere.
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I notice that this enforces RNAME compliance with the regexp regardless of any declared @HD-VN. Did HTSJDK consider making this check dependent on the file's VN header and allowing such RNAMEs in existing files with HD-VN≤1.5 or so? There was discussion in samtools/hts-specs#333 (comment) that it seems important not to gratuitously reject existing data files (if any…) while allowing for diagnostics on newly-produced files. |
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hmmm. this is a good point. will look into making is 1.5 and on only (not sure how....) |
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@jmarshall, we have decided (in htsjdk) to implement a blanket rejection of non-compliant sam files. if this turns out to be an undue burden on our users, we will consider putting to work to make htsjdk more version-aware. right now we are working on the next version which should include more version-aware features and it should be easier to do such a thing there...I still think that we were right to keep the SPEC version specific and not declare all old SAM files as non-compliant. |
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Fair enough. Please take a look at the text added in that new commit on samtools/hts-specs#333 too 😄 |
samtools/hts-specs#333