bamsort MC fix

This version fixes a bug in bamsort where empty MC aux fields were inserted for reads with unaligned mates. There is also a new program called bamfiltermc for removing such fields for from reads with unaligned mates.

bamsormadup empty MC tag fix

This version fixes a bug concerning the copying of empty CIGAR information fields from unmapped read mates.

bamsormadup blocksortverbose option updated

This version makes the blocksortverbose option in bamsormadup more specific.

bamsormadup blocksortverbose option

This version introduces the blocksortverbose option in bamsormadup.

bamsormadup merge stage memory control

Reduce memory consumption of bamsormadup in the merge stage.

bamdownsamplerandom index fix

bamdownsamplerandom now enables the hash parameter if indexing is enabled to avoid changing the sort ordering while sampling. Make sure to get the NON debug version for standard use.

Update to io_lib 1.14.8

This version updates the included io_lib to version 1.14.8 and fixes a bug concerning end of file detection on pipes.

Memory information for bamcat

bamcat prints information about memory usage at end of run starting from this version.

collation fix

This version fixes an issue with collation where similar read names were not considered distinct if they only differed by leading zeros in number representations.

Dynamic zlib loading support

This version introduces dynamic loading of alternative zlib implementations at run time. It uses the zlib for at https://github.com/cloudflare/zlib if the system supports the SSE4.2 and PCLMULDQ features (see http://www.htslib.org/benchmarks/zlib.html for samtools benchmarks using different zlib code bases).