A fix for undercounting the longest chain in discontiguous MB lookup table JIRA SB-4280

git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@103530 78c7ea69-d796-4a43-9a09-de51944f1b03

Author: boratyng

src/algo/blast/core/blast_nalookup.c

@@ -800,14 +800,18 @@ s_FillDiscMBTable(BLAST_SequenceBlk* query, BlastSeqLoc* location,
    longest_chain = 2;
    for (index = 0; index < mb_lt->hashsize / kCompressionFactor; index++)
        longest_chain = MAX(longest_chain, helper_array[index]);
-   mb_lt->longest_chain = longest_chain;
+    /* +1 because helper_array is not incremented for the first position of a
+      word */
+   mb_lt->longest_chain = longest_chain + 1;
    sfree(helper_array);
 
    if (kTwoTemplates) {
       longest_chain = 2;
       for (index = 0; index < mb_lt->hashsize / kCompressionFactor; index++)
          longest_chain = MAX(longest_chain, helper_array2[index]);
-      mb_lt->longest_chain += longest_chain;
+      /* +1 because helper_array2 is not incremented for the first position of a
+         word */
+      mb_lt->longest_chain += longest_chain + 1;
       sfree(helper_array2);
    }
    return 0;

src/algo/blast/unit_tests/api/ntlookup_unit_test.cpp

@@ -279,7 +279,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize11) {
 	BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length);
 	BOOST_REQUIRE_EQUAL(1, (int)lookup->template_type);
 	BOOST_REQUIRE_EQUAL(1, lookup->scan_step);
-	BOOST_REQUIRE_EQUAL(2, lookup->longest_chain);
+	BOOST_REQUIRE_EQUAL(3, lookup->longest_chain);
 	BOOST_REQUIRE_EQUAL(49, lookup->hashtable[2463300]);
 	BOOST_REQUIRE_EQUAL(392, lookup->hashtable[1663305]);
 	BOOST_REQUIRE_EQUAL(1049, lookup->hashtable[3586129]);
@@ -325,7 +325,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableCodingWordSize12) {
 	BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length);
 	BOOST_REQUIRE_EQUAL(3, (int)lookup->template_type);
 	BOOST_REQUIRE_EQUAL(1, lookup->scan_step);
-	BOOST_REQUIRE_EQUAL(2, lookup->longest_chain);
+	BOOST_REQUIRE_EQUAL(3, lookup->longest_chain);
 	BOOST_REQUIRE_EQUAL(3631, lookup->hashtable[133875]);
 	BOOST_REQUIRE_EQUAL(2092, lookup->hashtable[351221]);
 	BOOST_REQUIRE_EQUAL(4951, lookup->hashtable[1336356]);
@@ -371,7 +371,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize11) {
 	BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length);
 	BOOST_REQUIRE_EQUAL(2, (int)lookup->template_type);
 	BOOST_REQUIRE_EQUAL(1, lookup->scan_step);
-	BOOST_REQUIRE_EQUAL(2, lookup->longest_chain);
+	BOOST_REQUIRE_EQUAL(3, lookup->longest_chain);
 	BOOST_REQUIRE_EQUAL(36, lookup->hashtable[1353317]);
 	BOOST_REQUIRE_EQUAL(375, lookup->hashtable[1955444]);
 	BOOST_REQUIRE_EQUAL(5455, lookup->hashtable[1735012]);
@@ -417,7 +417,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableOptimalWordSize12) {
 	BOOST_REQUIRE_EQUAL(16, (int)lookup->template_length);
 	BOOST_REQUIRE_EQUAL(4, (int)lookup->template_type);
 	BOOST_REQUIRE_EQUAL(1, lookup->scan_step);
-	BOOST_REQUIRE_EQUAL(2, lookup->longest_chain);
+	BOOST_REQUIRE_EQUAL(3, lookup->longest_chain);
 	BOOST_REQUIRE_EQUAL(82, lookup->hashtable[9606485]);
 	BOOST_REQUIRE_EQUAL(752, lookup->hashtable[15622537]);
 	BOOST_REQUIRE_EQUAL(5408, lookup->hashtable[10084009]);
@@ -465,7 +465,7 @@ BOOST_AUTO_TEST_CASE(testDiscontiguousMBLookupTableTwoTemplatesWordSize11) {
 	BOOST_REQUIRE_EQUAL(1, (int)lookup->two_templates);
 	BOOST_REQUIRE_EQUAL(2, (int)lookup->second_template_type);
 	BOOST_REQUIRE_EQUAL(1, lookup->scan_step);
-	BOOST_REQUIRE_EQUAL(4, lookup->longest_chain);
+	BOOST_REQUIRE_EQUAL(6, lookup->longest_chain);
 	BOOST_REQUIRE_EQUAL(128, lookup->hashtable[1450605]);
 	BOOST_REQUIRE_EQUAL(342, lookup->hashtable[4025953]);
 	BOOST_REQUIRE_EQUAL(663, lookup->hashtable[3139906]);