%PDF-1.4 % 1 0 obj << /S /GoTo /D (section.1) >> endobj 4 0 obj (1 Introduction) endobj 5 0 obj << /S /GoTo /D (section.2) >> endobj 8 0 obj (2 Load the aligned reads and their sequences from a BAM file) endobj 9 0 obj << /S /GoTo /D (section.3) >> endobj 12 0 obj (3 Compute the original query sequences) endobj 13 0 obj << /S /GoTo /D (section.4) >> endobj 16 0 obj (4 Mismatches, indels, and gaps) endobj 17 0 obj << /S /GoTo /D (section.5) >> endobj 20 0 obj (5 Put the read sequences and reference sequences ``side by side'') endobj 21 0 obj << /S /GoTo /D (section.6) >> endobj 24 0 obj (6 OLD STUFF \(needs to be recycled/updated\)) endobj 25 0 obj << /S /GoTo /D (subsection.6.1) >> endobj 28 0 obj (6.1 Load paired-end reads from a BAM file) endobj 29 0 obj << /S /GoTo /D (section.7) >> endobj 32 0 obj (7 sessionInfo\(\)) endobj 33 0 obj << /S /GoTo /D [34 0 R /Fit ] >> endobj 45 0 obj << /Length 3071 /Filter /FlateDecode >> stream xZKH1*=g00Bo쁙e,o!?lKǗYΒU%/3O.=3ET"Oi]TIY6urL{Y㥚uZ]ҳ</d>C{,dv#^m;9|~_}?Q^ nD) MT*UNy07vy\楁{J4w r2WYJ$or=@1[s YTnyni) ?pޢxoRxɓ?FGHEfMtEVVeVULכJT$ Ε2inmo3H=t@D%EIؓݟYWӔgNNKMACxgIRH#6rj3L6[QcG| Ѥ $s]\*!H3AK}R`RZ63%hvRv#;~Ф>2zׯezz_r*덝rn3@XΦh _hdy`UƔN3u_9sc2n+08hy