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tree: 6bbe1609e1
Octocat-spinner-32 bcftools Adjust GT according to the most likely genotype (sites with multiple …
Octocat-spinner-32 examples removed downsample.c
Octocat-spinner-32 math added another type of LRT
Octocat-spinner-32 misc fixed compiling errors
Octocat-spinner-32 .gitignore updated .gitignore
Octocat-spinner-32 AUTHORS Imported from samtools-r902
Octocat-spinner-32 COPYING Imported from samtools-r902
Octocat-spinner-32 ChangeLog update changelog
Octocat-spinner-32 ChangeLog.old Imported from samtools-r902
Octocat-spinner-32 INSTALL update INSTALL
Octocat-spinner-32 Makefile removed sample
Octocat-spinner-32 NEWS Release samtools-0.1.18
Octocat-spinner-32 README.md * more README.md work
Octocat-spinner-32 bam.c 'B' now moves backward w.r.t. the query
Octocat-spinner-32 bam.h bugfix: wrong SP; missing DV in the VCF hdr
Octocat-spinner-32 bam2bcf.c bugfix: wrong SP; missing DV in the VCF hdr
Octocat-spinner-32 bam2bcf.h new BCF DV format: number of variant reads
Octocat-spinner-32 bam2bcf_indel.c Merge https://github.com/lh3/samtools into reduce
Octocat-spinner-32 bam2depth.c * updating help message for samtools depth
Octocat-spinner-32 bam_aux.c reduce BAM size (experimental)
Octocat-spinner-32 bam_cat.c added the "cat" command (by Chris Saunders)
Octocat-spinner-32 bam_color.c Adjust for leading hard clip on colorspace reads.
Octocat-spinner-32 bam_endian.h Imported from samtools-r902
Octocat-spinner-32 bam_import.c 'B' now moves backward w.r.t. the query
Octocat-spinner-32 bam_index.c Catch and report invalid BAM header, instead of segfaulting later on.
Octocat-spinner-32 bam_lpileup.c Imported from samtools-r902
Octocat-spinner-32 bam_mate.c fixed two gcc warnings
Octocat-spinner-32 bam_md.c Merge https://github.com/lh3/samtools into reduce
Octocat-spinner-32 bam_pileup.c Merge https://github.com/lh3/samtools into reduce
Octocat-spinner-32 bam_plcmd.c new BCF DV format: number of variant reads
Octocat-spinner-32 bam_qa.c print to output
Octocat-spinner-32 bam_reheader.c Imported from samtools-r902
Octocat-spinner-32 bam_rmdup.c Imported from samtools-r902
Octocat-spinner-32 bam_rmdupse.c Imported from samtools-r902
Octocat-spinner-32 bam_sort.c Allow max_mem for sort to be specified with units.
Octocat-spinner-32 bam_stat.c fixed a minor issue
Octocat-spinner-32 bam_tview.c Check lowerbound in text entry box to avoid segfault in tview. Remove…
Octocat-spinner-32 bamtk.c removed sample
Octocat-spinner-32 bedidx.c for WIN32 compatibility
Octocat-spinner-32 bgzf.c added bgzf_check_bgzf() (used by tabix)
Octocat-spinner-32 bgzf.h added bgzf_check_bgzf() (used by tabix)
Octocat-spinner-32 bgzip.c Imported from samtools-r902
Octocat-spinner-32 cut_target.c fixed a flaw in targetcut
Octocat-spinner-32 errmod.c Imported from samtools-r902
Octocat-spinner-32 errmod.h added comment
Octocat-spinner-32 faidx.c make faidx works with <2GB lines
Octocat-spinner-32 faidx.h Imported from samtools-r902
Octocat-spinner-32 kaln.c Imported from samtools-r902
Octocat-spinner-32 kaln.h Imported from samtools-r902
Octocat-spinner-32 khash.h updated khash.h to 0.2.5
Octocat-spinner-32 klist.h Imported from samtools-r902
Octocat-spinner-32 knetfile.c avoid a segfault when network connect fails
Octocat-spinner-32 knetfile.h Imported from samtools-r902
Octocat-spinner-32 kprobaln.c fixed a bug/typo
Octocat-spinner-32 kprobaln.h Imported from samtools-r902
Octocat-spinner-32 kseq.h update kseq.h to the latest version
Octocat-spinner-32 ksort.h Imported from samtools-r902
Octocat-spinner-32 kstring.c convert padded BAM to unpadded BAM
Octocat-spinner-32 kstring.h * fixing overflow/underflow in integer parsing
Octocat-spinner-32 padding.c rename pad2unpad to depad
Octocat-spinner-32 phase.c allow to change whether to drop ambiguous reads
Octocat-spinner-32 radix.h removed sample
Octocat-spinner-32 razf.c Imported from samtools-r902
Octocat-spinner-32 razf.h Imported from samtools-r902
Octocat-spinner-32 razip.c Imported from samtools-r902
Octocat-spinner-32 sam.c Check write filehandle after opening for write. tamw/tamr is a union …
Octocat-spinner-32 sam.h Imported from samtools-r902
Octocat-spinner-32 sam_header.c Allow user defined [lowercase] tags in header elements.
Octocat-spinner-32 sam_header.h Imported from samtools-r902
Octocat-spinner-32 sam_view.c scale depth to quality (hidden option)
Octocat-spinner-32 sample.c If there is only one RG tag present in the header and reads are not a…
Octocat-spinner-32 sample.h Imported from samtools-r902
Octocat-spinner-32 samtools.1 Release samtools-0.1.18
README.md

This is NOT the official repository of SAMtools.

The official SAMtools repository can be found at: http://samtools.sourceforge.net/

Major fixes:

- 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

Minor fixes:

- 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.
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