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* '''Current Release Notes''' (1/19/2011)
* '''Current Release Notes''' (1/19/2011)
** FASTQ
** Added the following programs:
*** Add option to disable the unique sequence identifier check since that uses a lot of memory.
*** mgpileup
*** thunderVCF
*** vcfCooker
*** verifyBamID
** BAM
*** Fixed bug in SamQuerySeqWithRefIter
*** Add handling of the reference to the SAM Library to allow the conversion of SAM Record Sequence to/from using '=' or just bases.
**** Add the conversion to/from '=' in the sequence to the bam Convert program.
*** Add the ability to read the header when opening a BAM/SAM file.
*** Update SetReadSection to reset the data for validating sorting since it can jump around in the file.
** GLF
** GLF
*** Automatically write the End Maker record when writing GLF files.
*** Fixed bug that incorrectly wrote GLF Records of type 2
*** Add capability of consuming records to get to the next reference section.
*** Add capability to consume remaining records when getNextRefSection is called. Also when writing automatically write the End Marker if it was not already written when a new RefSection is written or when the file is closed.
*** Fixed bug in writing GLF records of type 2.
** FastQ
** Other
*** Add option to not check for uniqueness of the sequence identifier
*** Remove ZLIB from being contained within the repository (having zlib in the repository may have caused some compile issues in the previous version).
** OTHER
*** removed zlib from being included in the repository.
=== Problems in Current Release ===
=== Problems in Current Release ===
