[Samtools-announce] Picard Release 1.29

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

Hi Folks,

OK, this has been fixed.  Sorry for any inconvenience.

Picard release 1.29
18 August 2010

- Fixed incorrect use of 
BlockCompressedFilePointerUtil.areInSameOfAdjacentBlocks that would 
result in incorrect results for some calls to BAMFileReader.query methods.

-Alec

On 8/18/10 11:35 AM, Alec Wysoker wrote:
> 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
>>