Trace mismatches outside known SNP positions to call new SNPs with current distance algorithm (distance.go).
Add prior prob for new SNP location.
Fix a bug of assigning prior prob to new SNPs: assign prior prob (=epsilon) to the first aligned base which is considered as new SNP.
Test calculation of SNP quality for various values of EPSILON
Remove SNP_Pos from SNP_Prof data structure and update SNP call positions during alignment steps (callsnp.go).
Take into account SNP/Indel rate in calculation of distance threshold (callsnp.go).
Change value of EPSILON to 0.01 (share.go).
Add trace back of 'edit distance part' of alignment to call new SNPs
Re-assign prior prob, check for empty SNPs before putting to results.
Copy aligned-base-as-SNP from reads to release memory for reads.
Update SNP quality test
Fix a bug when checking SNP length
Call SNPs with only alignment with minimum distance
Use max_match=16, fixed dis_thres at 5, take into account all base diff with indel alignment
Change prior prob, dis thres
Print alignment pos
Get log info, clean code, fix the bug when reading input reads
revised debug info
Fix the bug of incorrectly reading reads.
Consider qualities in reverse order when using reverse complements of reads.
...
Fix bug: allocate memory for read info
fix bug, add info...
Fix the bug of reading input (need to adjust length of variable to the length of input).
Add functions for outputing debug info to files.