Lancet release v1.1.0

New release with:

1. Support for variant calling on 10x Genomics linked-reads sequencing data (via --linked-reads,-J parameter).
2. Somatic variants on multiple haplotypes are flagged with the "MulitHP" in the FILTER column.
3. Haplotypes read counts for the ref and alt alleles reported using HPR and HPA respectively in the FORMAT field.
4. List of barcodes supporting the variants are also reported in the FORMAT field.

Lancet release v1.0.7

Minor release that:

1. supports a new command line parameter to request only primary alignments to be used for variant calling;
2. supports complex events: multiple consecutive snv, ins, del at a locus reported in the output VCF a a single replacement operation event;
3. includes a new parameter to control AS and XS difference when selecting read alignments;
4. implements better type support when extracting tags from sam alignments;
5. automatically turns off the active region module if MD tags are missing from the BAM file;
6. includes updated APIs: htslib v1.8 and bamtools v2.5.1;

Lancet release v1.0.6

Minor release that:

1. fixes a bug causing a rare "inf" in FET score calculation;
2. adds the command line executed in the VCF header;
3. reports warning message if MD tags are missing from alignments.

Lancet release v1.0.5

Minor release that fixes a bug causing segmentation fault in same cases when processing reads with different lengths.

Lancet release v1.0.4

Fixed minor compilation bug

Lancet release v1.0.3

Minior release which add support for padding in input regions and fixes a couple of small formatting issues in the out VCF.

Lancet release v1.0.2

added support for single chromosome labels in --reg option (e.g --reg 22)

Lancet release v1.0.1

Update readme with bioRxiv citation; update version number 1.0.1

lancet release v1.0.0

fix minor leak by destroying faidx after usage since htslib doesn't s…

…eem to cope with a large number of open reference file indexes