Details
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Bug
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Status: Open
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Major
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Resolution: Unresolved
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AStalavista 4.0 (API 1.30)
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None
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None
Description
In Astalavista 4.0 the Scorer tool no longer includes information about the splice site type in the output VCL file (e.g. TYPE=U2_GTAG). It only includes the mode (MOD=CON or MOD=ALT).
In Astalavista 3.2 (API 1.22) it did include the "TYPE=" field in the output VCL.
Example output (splice sites are the same in both VCLs):
Astalavista 3.2 VCL:
3R 835491 835491^3R ATATGTATCCTTA . 5.590205 PASS TYPE=U12_GTAG;MOD=CON;
3R 869486 869486-3R GGTCGTTCTATATTTAAACCCAATAGACTTA . -Infinity q-1000 TYPE=UNKNOWN;MOD=CON;
3R 869548 869548^3R TAAGGTAAGCTTA . 5.725247 PASS TYPE=U2_GTAG;MOD=CON;
3R 895786 895786-3R TTGACCTTTATAATTTAAAATTTCAGCAAAC . -Infinity q-1000 TYPE=UNKNOWN;MOD=CON;
Astalavista 4.0 VCL:
3R 835491 835491^3R ATGTATCCTT . -20002.342 q-1000 MOD=CON;
3R 869486 869486-3R GTCGTTCTATATTTAAACCCAATAGACT . 3.4419343 PASS MOD=CON;
3R 869548 869548^3R AGGTAAGCTT . -10003.402 q-1000 MOD=CON;
3R 895786 895786-3R TGACCTTTATAATTTAAAATTTCAGCAA . 3.1529703 PASS MOD=CON;