CSI index decoding

This version introduces capabilities for using CSI indexes in range decoding.

bammaskflags auxexists

This version adds the auxexists option for bammaskflags.

CSI indexing

This version introduces CSI indexing for BAM files.

Allow larger positions in SAM parsing

2.0.84-release-20180223152609

Release 2.0.84-release-20180223152609

bamsort queryname_HI mode

This version introduces the queryname_HI sort order in bamsort taking the HI aux field into account for alignments with the same query name.

bamsormadup fix

This version fixes a bug in bamsormadup resulting in an endless recursion.

Sorting by tag in bamsort

The bamsort program has a new sort order SO=tag for sorting files by an aux field storing string values. This is useful for collating reads sharing a common tag.

rcsupport in bamsormadup

This version adds the rcsupport flag in bamsormadup for adding the rc aux tag (unclipped read coordinate)

Add mc field in bammarkduplicatesopt

This version adds the mc aux field in bammarkduplicatesopt if the addmatecigar option is set.

bamfillquery

This release adds the tool bamfillquery to inject query sequences into alignment files with undefined query sequences.