The official SAMtools repository can be found at: http://samtools.sourceforge.net/
- added "samtools sample" command, to sample reads from a SAM/BAM file at a given frequency. - added "samtools qa" command, to compute the mean and median coverage, as well a histogram from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX. Furthermore, "other" information is also available in the output file, namely: - Total number of reads - Total number of duplicates found and ignored (duplicates are "found" based on the sam flag and are ignored in the counting of coverage) - Percentage of unmapped reads - Percentage of zero quality mappings - Number of proper paired reads (based on sam flag of proper pairs) - Percentage of proper pairs.e
- Check the write filehandle after opening for write. - allow for user defined [lowercase] tags in header elements. - allow the maximum memory for "samtools sort" to be specified with units. - adjust for leading hard clip on colorspace reads. - catches and reports an invalid BAM header, instead of segfaulting later on. - fixes a small underflow/overflow bug in integer parsing. - checks for a lowerbound in text entry box to avoid segfault in tview.