Tangram_bam concatenates special references for ssw
Shrink tangram_bam pool; decrease the number of reads for SSW
tangram_bam handles the target region
Erase the alignments that are found by their mates in the target region.
Merge branch 'master' of github.com:jiantao/Tangram
Add TB_VERBOSE_DEBUG for tangram_bam files
Use bam index jumping
Fix the BamRegion setting
Set the RightPosition of BamRegion
"chr" is unnecessary in vcf
Add TD_VERBOSE_DEBUG and keep SpRefID in pSpecialData
SeqTransfer shouldn't be an inline function since there is a loop.
Add GetSpRefConcatenatedPos function
Move SeqTransfer from the header file to cpp file
Add ReverseSeqToString
Report ALT sequences if possible
Tangram_bam: remove option 'z' and add option 't'; fix too much memory usage
Tangram_detect: reverse complete fix for orphand mates; fix failLimit for second partial alignments
If the original both mates are soft-clipped, then don't mark both of them
as unmapped.
Handle whole-genome tangram_bam
Update tangram_bam help list