Re: [Samtools-announce] Picard release 1.28 -- Please wait before downloading!

[Alec W. <al...@br...>]

Hi Folks,

We just discovered a bug in BAM queries.  Please do not use this 
version.  Fix will arrive in a few minutes.

-Alec

On 8/18/10 10:16 AM, Alec Wysoker wrote:
> Picard Release 1.28
> 18 August 2010
>
> - In various programs, write messages to stderr rather than stdout, so that BAM output can be sent to stdout.
>
> - BlockCompressedFilePointerUtil: encapsulate code for manipulating BGZF virtual file pointers.  Make sure it works for virtual file pointer that is so large as to be negative as signed long.
>
> - BamToBfq: Added option to write only the first N bases of the read to the bfq file.
>
> - CigarUtil: Added method to add soft-clipped bases to either end of a cigar (used when reads have been trimmed before alignment and the cigar needs to be adjusted to reflect this).
>
> - AlignmentMerger: Added option to specify reserved tags from alignment bam to bring over when merging.
>
> - SamRecord: Change mAttributes from ArrayList to custom linked list to reduce memory footprint.
>
> - SamFileValidator: Added some progress logging.
>
> - DuplicationMetrics: Change to allow calculation of estimated library size in heavily duplicated (as in 99%+ duplicaiton) data.
>
> - MergeBamAlignment: Clarified documentation to make clear that a sequence dictionary is expected in the same directory as the reference fasta and that its extension should be .dict.
>
>
>
> -Alec
>