I have tried to use ncbi blast 2.3.0 version which support output sam file.
I did it like below,
/program/ncbi-blast-2.3.0+/bin/blastn -db /db/class2.db -max_target_seqs 1 -outfmt 17 -query ./S4--S4.fasta -out ./S4--S4.sam
Then I got strange results that first all reference Name and Query Name is wrongly generated.
For example.expected name
queryname = m160213_235908_42273_c100966372550000001823205304301641_s1_p0/32769/0_2213 0.89 28 Reference name = HLA_HLA00688_DRB1_04_03_01_15246_bp
Query name = BL_ORD_ID:16 Reference Name : Query_1
And also there is no sequences are generated only Cigar , position, Map Quality, I want to put sequences also,
Do you have any idea how to handle blast with output as SAM file?