Adapter clipping generalisation

This version introduces adapter clipping capabilities for BAM files in which not all reverse complement flags are unset (e.g. for pre-aligned data).

duplicate flag set/reset

This release changes the behavior of bammarkduplicates and bammarkduplicates2 in the sense that the duplicate flag is erased for alignments which are not considered duplicates. Previously the duplicate flag was only added for duplicate alignments but left as is for any other alignments.

bamcollate2 pass-through

This release allows an empty exclude parameter in bamcollate2. It also introduces more checking in bam12auxmerge (implemented by Andrew Whitwham).

Fixed order in header attributes when rewriting RG lines

This version introduces ordering the attributes of rewritten RG lines in bamcollate2 along the order given in the SAM spec to avoid confusion for programs which expect ID to be the first such attribute in each RG line.

Please note: the binary archive was replaced on January 17th 2015, as the previous archive contained a version of io_lib compiled with GCC optimization level -O3, which lead to crashes when outputting data in the SAM format.

Read group id rewriting in bamcollate2

This version introduces read group id rewriting in bamcollate2. The binaries in the archives below are linked against io_lib version 1.13.8 instead of the previous version 1.13.7, which had known issues decoding some CRAM files.

bamseqchksum additional hash digests

This release introduces new hash digests in bamseqchksum.

streaming duplicate marking fix

This is a bug fix release correcting an issue in streaming duplicate marking where some reads at the end of a file could be dropped.

Base quality histogram in bamvalidate

In this release the basequalhist option is added for bamvalidate.

Output file splitting support for bamtofastq

This release adds the split option for bamtofastq. Named output files (plain or gzip compressed) can be split into chunks of a given number of reads.

tag support in duplicate marking

This release adds tag support for bammarkduplicates and bammarkduplicates2. String tags in auxiliary fields can be used to place reads or read pairs in separate classes. Reads or read pairs will only be considered as duplicates if they have the same tag.