CHANGES IN VERSION 1.12.0 ------------------------ NEW FEATURES o Added a number of new features to featureCounts read summarization function, including reordering of reads in BAM files to make reads from the same pair be adjacent to each other, support for chromosome aliases and output of complete annotation data for counting results from meta-feature level summarization. o It is described in more details in the Users Guide on how featureCounts program summarizes reads. o Improved short indel detection for both Subread (align function) and Subjunc aligners. This was achieved by building a consensus indel table and by realigning the reads. Discovered indels are reported in the output in addition to the read mapping results. o Support for detection of long indels (up to 200bp) was added in Subread. When the specified value of `indels' argument is greater than 16, Subread will automatically perform read assembly to detect long insertions and deletions. o Subread and Subjunc can now take FASTQ/FASTA, SAM and BAM files as input and output mapping results in both SAM and BAM formats. o Subjunc now directly operates on raw read data (it previously took Subread output as input), thus reducing running time by nearly half. o Subjunc can be instructed to output uniquely mapped reads. Hamming distance and mapping quality scores can be used to break ties when more than one best location was found. o More options were added to exactSNP program. Its documentation was also greatly improved. o A number of bug fixes. CHANGES IN VERSION 1.10.0 ------------------------ NEW FEATURES o Rsubread package can now run on Mac OS X operating systems. o Major updates to the function 'featureCounts', a general-purpose read summarization function. CHANGES IN VERSION 1.8.0 ------------------------ NEW FEATURES o Fine-tuning of read alignment function (align) and exon-exon junction detection function (subjunc). o Major update to SNP calling algorithm (now use Fisher' exact tests to call SNPs). o More efficient implementation for removing duplicated reads (eg. supporting multi-threads and using less memory). CHANGES IN VERSION 1.6.0 ------------------------ NEW FEATURES o Significant improvement on the exon-exon junction detection (subjunc function). o Calling SNPs using a simple allele fraction approach (callSNPs function) . o Removing duplicated reads (removeDupReads function).