SWIPE 2.1.1: Fix for very long header strings in databases

Author: torognes

CHANGES

@@ -1,3 +1,7 @@
+2021-06-28  Torbjorn Rognes  <torognes@ifi.uio.no>
+        * Version 2.1.1
+        * Fix for very long header strings in NCBI database files
+
 2018-05-04  Torbjorn Rognes  <torognes@ifi.uio.no>
 	* Version 2.1.0
         * Fix for changes to NCBI database format

README

@@ -1,7 +1,7 @@
 SWIPE
 Smith-Waterman database searches with Inter-sequence Parallel Execution
 
-Copyright (C) 2008-2014 Torbjorn Rognes, University of Oslo, 
+Copyright (C) 2008-2021 Torbjorn Rognes, University of Oslo,
 Oslo University Hospital and Sencel Bioinformatics AS
 
 This program is free software: you can redistribute it and/or modify
@@ -105,7 +105,8 @@ specified organisms.
 SWIPE accepts only databases prepared using the formatdb or makeblastdb
 tools that are distributed together with NCBI BLAST and BLAST+. They
 can be downloaded at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/
-from NCBI.
+from NCBI. For makeblastdb, please use the "-blastdb_version 4" option
+to make databases that are compatible with SWIPE.
 
 The SWIPE distribution includes executable binaries for 64-bit Linux and
 Mac. SWIPE may be compiled from sources using either the GNU g++ compiler,

asnparse.cc

@@ -2,7 +2,7 @@
     SWIPE
     Smith-Waterman database searches with Inter-sequence Parallel Execution
 
-    Copyright (C) 2008-2013 Torbjorn Rognes, University of Oslo,
+    Copyright (C) 2008-2021 Torbjorn Rognes, University of Oslo,
     Oslo University Hospital and Sencel Bioinformatics AS
 
     This program is free software: you can redistribute it and/or modify
@@ -194,7 +194,27 @@ void parse_visiblestring(apt p)
       length = (length << 8) | p->ch;
       nextch(p);
     }
-  else if (p->len > 0x82)
+  else if (p->len == 0x83)
+    {
+      length = p->ch;
+      nextch(p);
+      length = (length << 8) | p->ch;
+      nextch(p);
+      length = (length << 8) | p->ch;
+      nextch(p);
+    }
+  else if (p->len == 0x84)
+    {
+      length = p->ch;
+      nextch(p);
+      length = (length << 8) | p->ch;
+      nextch(p);
+      length = (length << 8) | p->ch;
+      nextch(p);
+      length = (length << 8) | p->ch;
+      nextch(p);
+    }
+  else if (p->len > 0x84)
     {
       fprintf(stderr, "Error: illegal string length (%02x).\n", p->len);
       fatal("Error parsing binary ASN.1 in database sequence definition.");

swipe.h

@@ -2,7 +2,7 @@
     SWIPE
     Smith-Waterman database searches with Inter-sequence Parallel Execution
 
-    Copyright (C) 2008-2014 Torbjorn Rognes, University of Oslo, 
+    Copyright (C) 2008-2021 Torbjorn Rognes, University of Oslo,
     Oslo University Hospital and Sencel Bioinformatics AS
 
     This program is free software: you can redistribute it and/or modify
@@ -55,7 +55,7 @@
 #define LINE_MAX 2048
 #endif
 
-#define SWIPE_VERSION "2.1.0"
+#define SWIPE_VERSION "2.1.1"
 
 // Should be 32bits integer
 typedef unsigned int UINT32;