[Sashimi-commit] SF.net SVN: sashimi:[9473] trunk/trans_proteomic_ pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp

[<en...@us...>]

Revision: 9473
          http://sourceforge.net/p/sashimi/code/9473
Author:   eng_jk
Date:     2026-02-25 18:09:39 +0000 (Wed, 25 Feb 2026)
Log Message:
-----------
modify DatabaseParser to account for Comet .idx extension

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp

Modified: trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp	2025-12-09 06:49:19 UTC (rev 9472)
+++ trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp	2026-02-25 18:09:39 UTC (rev 9473)
@@ -65,6 +65,12 @@
 	    memcpy(current_database, 
 		   tag->getAttributeValue("local_path"), 
 		   strlen(tag->getAttributeValue("local_path"))+1);
+
+       // when parsing .idx from Comet index search, strip ".idx" extension from
+       // parsed attribute value to return original fasta for sequence matching
+       int len = strlen(current_database);
+       if (strcmp(current_database + len - 4, ".idx") == 0 && len >= 4)
+          current_database[len - 4] = '\0';
 	  }
 	  else if(tag->isStart() && ! strcmp(tag->getName(), "database_refresh_timestamp")) {
 	    strcpy(current_database, tag->getAttributeValue("database"));

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