LeftAlignIndels Alignments added out of order issue when reads are fed in coordinate sorted order.

[gokalpcelik]

Hi team.
This is an old topic from the forum

LeftAlignIndels Alignments added out of order... Offending records are at [chr7:55268881] and [chr7:55268881]

java.lang.IllegalArgumentException: Alignments added out of order in SAMFileWriterImpl.addAlignment for file:///Users/jcovino/Desktop/PLAA_2390/broken.bam. Sort order is coordinate. Offending records are at [chr7:55268881] and [chr7:55268881]
at htsjdk.samtools.SAMFileWriterImpl.assertPresorted(SAMFileWriterImpl.java:212)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:199)
at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyWrite(AsyncSAMFileWriter.java:36)
at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyWrite(AsyncSAMFileWriter.java:16)
at htsjdk.samtools.util.AbstractAsyncWriter$WriterRunnable.run(AbstractAsyncWriter.java:123)
at java.base/java.lang.Thread.run(Thread.java:840)

The only current solution to this problem is feeding reads in queryname sorted way. When reads are coordinate sorted this error occurs.

There is a request from users that this tool should be able to work with coordinate sorted reads.