SAMUtils:getOtherCanonicalAlignments extract 'SA' tag and return a list of supplementary alignments #685

lindenb · 2016-08-16T14:49:24Z

Description

I've added a new function `getOtherCanonicalAlignments` in SAMUtils. This function is used to extract the 'SA' tag of a SAMRecord as a `List<SAMRecord>`of supplementary alignements.

    /**
     * Extract a List of 'other canonical alignments' from a SAM record. Those alignments are stored as a string in the 'SA' tag as defined
     * in the SAM specification.
     * Each record in the List is a non-paired read.
     * The name, sequence and qualities are copied from the original record
     * The SAM flag is set to <code>SUPPLEMENTARY_ALIGNMENT (+ READ_REVERSE_STRAND )</code>
     * @param record must be non null and must have a non-null associated header.
     * @return a list of 'other canonical alignments' SAMRecords. The list is empty if the 'SA' attribute is missing.
     */
public static List<SAMRecord> getOtherCanonicalAlignments(final SAMRecord record)

testOtherCanonicalAlignments was added to SAMUtilsTest ( create one read with SA flag, check the values of the supplementary alignments)

PS: The SA tag is defined in the spec as

Other canonical alignments in a chimeric alignment, formatted as a semicolon-delimited list: (rname,pos,strand,CIGAR,mapQ,NM;)+. Each element in the list represents a part of the chimeric alignment.

Checklist

Code compiles correctly
New tests covering changes and new functionality
All tests passing
Extended the README / documentation, if necessary
Is not backward compatible (breaks binary or source compatibility)

coveralls · 2016-08-16T15:01:30Z

Coverage increased (+0.02%) to 68.827% when pulling 1a8c36a on lindenb:sam_xa into c8202f2 on samtools:master.

coveralls · 2016-08-16T15:01:30Z

Coverage increased (+0.03%) to 68.833% when pulling 1a8c36a on lindenb:sam_xa into c8202f2 on samtools:master.

coveralls · 2016-08-16T15:13:07Z

Coverage increased (+0.02%) to 68.827% when pulling 1a8c36a on lindenb:sam_xa into c8202f2 on samtools:master.

droazen · 2016-08-16T15:21:58Z

@jamesemery could you please review?

coveralls · 2016-08-17T09:09:55Z

Coverage increased (+0.03%) to 68.835% when pulling de3873f on lindenb:sam_xa into c8202f2 on samtools:master.

jamesemery · 2016-08-17T13:19:36Z

src/main/java/htsjdk/samtools/SAMUtils.java

+                (commaStrs[2].equals("+") ? 0 : SAMFlag.READ_REVERSE_STRAND.flag) );
+            otherRec.setCigar( TextCigarCodec.decode( commaStrs[3] ) );
+            otherRec.setMappingQuality( Integer.parseInt(commaStrs[4]) );
+            otherRec.setAttribute( SAMTagUtil.getSingleton().NM , Integer.parseInt(commaStrs[5]) );                  


All of these .parseInt() calls open the possibility of breaking on bad input and exposing a stack trace to the user. Perhaps you should emit a SAMException if any of these fields don't parse correctly?

lindenb · 2016-08-17T20:11:09Z

Thank you for the review and back to you @jamesemery

I've considered the mate
surrounded parseInt with try catch
considered the first suppl alignment if the read is supplementary
moved the Pattern out of the function.
updated the test

NB: I'll be away from github for a few days.

coveralls · 2016-08-17T20:15:59Z

Coverage increased (+0.03%) to 68.841% when pulling 899227b on lindenb:sam_xa into c8202f2 on samtools:master.

jamesemery · 2016-08-19T16:38:37Z

@droazen These changes look good to me

lbergelson · 2016-08-25T14:30:26Z

Thanks @lindenb and @jamesemery

lindenb added 3 commits August 16, 2016 16:36

extract suppl alignments

31b7195

typo

c100ed8

variable name

1a8c36a

strand

de3873f

jamesemery reviewed Aug 17, 2016
View reviewed changes

fix PR

899227b

lbergelson merged commit c3d5a88 into samtools:master Aug 25, 2016

jamesemery mentioned this pull request Aug 25, 2016

Add API support for SA tags broadinstitute/gatk#2115

Closed

lindenb deleted the sam_xa branch August 25, 2016 19:39

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

SAMUtils:getOtherCanonicalAlignments extract 'SA' tag and return a list of supplementary alignments #685

SAMUtils:getOtherCanonicalAlignments extract 'SA' tag and return a list of supplementary alignments #685

SAMUtils:getOtherCanonicalAlignments extract 'SA' tag and return a list of supplementary alignments #685

SAMUtils:getOtherCanonicalAlignments extract 'SA' tag and return a list of supplementary alignments #685

Conversation

Description

I've added a new function getOtherCanonicalAlignments in SAMUtils. This function is used to extract the 'SA' tag of a SAMRecord as a List<SAMRecord>of supplementary alignements.

Checklist

Choose a reason for hiding this comment

I've added a new function `getOtherCanonicalAlignments` in SAMUtils. This function is used to extract the 'SA' tag of a SAMRecord as a `List<SAMRecord>`of supplementary alignements.