expGetSeq
---------

This is the partial source of a program that reads a trace file, clips
it, then outputs the sequence and clipped points in squirrel experiment
file format.  The clipping is performed using LaDeana's quality
measures. If a trace failes to meet the overall quality criterion, QL
is 0 and QR is 1. Sources for this are in ../newted. Example of
output:


SQ
     AG--TGCATG CCTGCAGGTC GACTCTAGAG G-TCCCGGGG TACCGAGCTC GAATTC-TAA
     TCATGGTCAT AGCTGT-TCC TGTGTGAAAT T-TTATCCGC TCACAATTCC ACACAACATA
     CGAGCCGGAA GCATAAAGTG TAAAGCCTGG GGTGCCTAAT GAGTGAGCTA ACTCACATTA
     ATTGCGTTGC GCTCACTGCC CGCTTTCCAG TCGGGAAACC TGTCGTGCCA GCTGCATTAA
     TGAATCGGCC AACGCGCGGG GAGAGGCGGT TTGCGTATTG GGCGCCAGGG TGGTTTTA-T
     TTTCACCAGT GAGACGGGCA ACAGCTGATT GCCCTTCACC GCCTGGCCCT GAGAGGAGTT
     GCAGCAAGCG GTCCACGCT- GTT-TGCCCC AGCAGGCG-A AATCCTGTTT TGATGGTTGG
     TTCC-GAAAT CGGCAAAAAT CCCTTATAAA TTC-AAAGGA TAGG-CCGAG --TGGGG-T-
     AGTTTTT-TT TCCGG-TTTG AACAAGT-GT TCCCCTGTT- AAAGGA-CGT GGG--TC-AA
     CCGTT-AAA- GGG-G--AA- -CCGTTTT-T TTATGGG--A --GGC---TT -C--GTTCCG
     TTA-CCTG-T T-AA-GTTTT TTTGGGGTT- TGG-G-CGTA AG-GCT-AAT -GGACC-TAA
     TGG-GGCCC- GATTTTGGGT T-TGGGGGAA GCGGA--GAC GG-GG-TG-G TGGGTGTAT-
     GGA-GTC--G -TTAGG-TGG GAAT--T-GG TG--T-GG-- ATCG-TT-G- -T--GGTTTT
     T-GGT-T-TA GGGGTGGTT  --GTGTTTTT T-GTGT-TTG --TT--T
//
QL   8
QR   329


*** 28-Jul-92
Overall quality checking has now been turned off.
Reinvoke using the -DQUAL_CHECK compilation flag.