35 lines
1.5 KiB
Plaintext
35 lines
1.5 KiB
Plaintext
expGetSeq
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---------
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This is the partial source of a program that reads a trace file, clips
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it, then outputs the sequence and clipped points in squirrel experiment
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file format. The clipping is performed using LaDeana's quality
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measures. If a trace failes to meet the overall quality criterion, QL
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is 0 and QR is 1. Sources for this are in ../newted. Example of
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output:
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SQ
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AG--TGCATG CCTGCAGGTC GACTCTAGAG G-TCCCGGGG TACCGAGCTC GAATTC-TAA
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TCATGGTCAT AGCTGT-TCC TGTGTGAAAT T-TTATCCGC TCACAATTCC ACACAACATA
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CGAGCCGGAA GCATAAAGTG TAAAGCCTGG GGTGCCTAAT GAGTGAGCTA ACTCACATTA
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ATTGCGTTGC GCTCACTGCC CGCTTTCCAG TCGGGAAACC TGTCGTGCCA GCTGCATTAA
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TGAATCGGCC AACGCGCGGG GAGAGGCGGT TTGCGTATTG GGCGCCAGGG TGGTTTTA-T
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TTTCACCAGT GAGACGGGCA ACAGCTGATT GCCCTTCACC GCCTGGCCCT GAGAGGAGTT
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GCAGCAAGCG GTCCACGCT- GTT-TGCCCC AGCAGGCG-A AATCCTGTTT TGATGGTTGG
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TTCC-GAAAT CGGCAAAAAT CCCTTATAAA TTC-AAAGGA TAGG-CCGAG --TGGGG-T-
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AGTTTTT-TT TCCGG-TTTG AACAAGT-GT TCCCCTGTT- AAAGGA-CGT GGG--TC-AA
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CCGTT-AAA- GGG-G--AA- -CCGTTTT-T TTATGGG--A --GGC---TT -C--GTTCCG
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TTA-CCTG-T T-AA-GTTTT TTTGGGGTT- TGG-G-CGTA AG-GCT-AAT -GGACC-TAA
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TGG-GGCCC- GATTTTGGGT T-TGGGGGAA GCGGA--GAC GG-GG-TG-G TGGGTGTAT-
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GGA-GTC--G -TTAGG-TGG GAAT--T-GG TG--T-GG-- ATCG-TT-G- -T--GGTTTT
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T-GGT-T-TA GGGGTGGTT --GTGTTTTT T-GTGT-TTG --TT--T
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//
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QL 8
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QR 329
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*** 28-Jul-92
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Overall quality checking has now been turned off.
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Reinvoke using the -DQUAL_CHECK compilation flag.
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