VerifyBamID Versions Save

ChangeLog:

1. Change to only output top 10 dims for UD and V matrices.
2. Update citation and reorg description
3. Update citation author list
4. Add exome region markers based on 1000g phase3 build37 reference
5. Adjust PCs reporting format in ".Ancestry" file
6. Update both b37 and b38 exome resource files
7. Update output format description
8. Resolved compilation errors in macOS Catalina
9. Update readme and verbose output format
10. Remove redundant chrom prefix in hgdp.10k.b38.vcf.gz.dat.bed file
11. Rename SimpleMpileup function
12. Expose several pileup parameters to cmdline arguments
13. Update cmdline help info in README.md
14. Add docker hub pull badge
15. Bump version number to distinguish from VB1

ChangeLog:

1. Adding Dockerfile;
2. Fix bug when disabling sanity check function;
3. Update README.md;
4. Remove 1000g phase1 resource files;
5. fix a bug in hgdp.100k.b37.vcf… resource files;
6. fix hgdp V file dimensions;
7. Remove online libhts compiling;
8. Update readme to add help information;
9. Update CMake cmdline variable names;
10. Output version information;

1. Fix bug in parsing sample name
2. update SVDcalculator warnings for non-auotosome markers
3. Add information output for the number of markers in ref matrix
4. Fixed output information of total input number of marker

1. Fix bug in PileupFile input routine

Note: Since this version, we introduce marker quality checking function, you can use --DisableSanityCheck to disable this feature.

Update:

1. Add result format backward compatibility
2. Fix Pileup output format
3. Set use_orphan_read as default
4. Add Pileup format as input option

We updated the output format and also generated output files that are compatible with verifyBamID1. We also introduced epsilon parameter to control the convergence speed, you can decide your own threshold based on the trade-off between speed and accuracy.