Release/1.2.0

ToniWestbrook · Mar 28, 2016 · ee1895c · ee1895c
1 parent 3a44a6c
commit ee1895c
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Showing 4 changed files with 12 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Change Log
 
+## [1.2.0] - 2016-03-27
+### Added
+- New columns in UniProt report related to database cross-references (KEGG, NCBI, PATRIC, Ensembl)
+- Added experimental support/fix for shared memory indexed references
+
 ## [1.1.0] - 2015-11-08
 ### Added
 - Option for preparing a pre-downloaded and/or pre-indexed reference.  This will skip the download and clean any applicable portion of the reference/index

diff --git a/bwa.c b/bwa.c
@@ -327,7 +327,8 @@ int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
 		idx->bns->anns[i].name = (char*)(mem + k); k += strlen(idx->bns->anns[i].name) + 1;
 		idx->bns->anns[i].anno = (char*)(mem + k); k += strlen(idx->bns->anns[i].anno) + 1;
 	}
-	idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;
+	//idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;
+	idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac+1;
 	assert(k == l_mem);
 
 	idx->l_mem = k; idx->mem = mem;
@@ -366,7 +367,8 @@ int bwa_idx2mem(bwaidx_t *idx)
 	free(idx->bns->anns);
 
 	// copy idx->pac
-	x = idx->bns->l_pac/4+1;
+	//x = idx->bns->l_pac/4+1;
+	x = idx->bns->l_pac+1;
 	mem = realloc(mem, k + x);
 	memcpy(mem + k, idx->pac, x); k += x;
 	free(idx->bns); idx->bns = 0;

diff --git a/main.h b/main.h
@@ -65,7 +65,7 @@
 #ifndef PACKAGE_VERSION
 #define PACKAGE_VERSION STR(PACKAGE_VERSION_MAJOR) "." STR(PACKAGE_VERSION_MINOR) "." STR(PACKAGE_VERSION_REV)
 #define PACKAGE_VERSION_MAJOR 1
-#define PACKAGE_VERSION_MINOR 1
+#define PACKAGE_VERSION_MINOR 2
 #define PACKAGE_VERSION_REV 0
 #endif
 

diff --git a/uniprot.c b/uniprot.c
@@ -86,7 +86,7 @@ void renderUniprotReport(int passType, int passPrimary, FILE * passStream) {
 			break;
 
 		case OUTPUT_TYPE_UNIPROT_FULL:
-			fprintf(passStream, "Count\tAbundance\tUniProtKB\tID\tOrganism\tProtein Names\tGenes\tPathway\tFeatures\tGene Ontology\tReviewed\tExistence\tComments\n");
+			fprintf(passStream, "Count\tAbundance\tUniProtKB\tID\tOrganism\tProtein Names\tGenes\tPathway\tFeatures\tGene Ontology\tReviewed\tExistence\tComments\tCross Reference (KEGG)\tCross Reference (GeneID)\tCross Reference (PATRIC)\tCross Reference(EnsemblBacteria)\n");
 			renderUniprotEntries(uniprotLists + UNIPROT_LIST_FULL, UNIPROT_LIST_FULL, passStream);
 			freeCURLBuffer(&tempBuffer);
 
@@ -297,7 +297,7 @@ void retrieveUniprotOnline(UniprotList * passList, CURLBuffer * retBuffer) {
 			}
 
 			// Stage 3 - Retrieve Results
-			sprintf(queryString, "query=job:%s&format=tab&columns=entry%%20name,id,organism,protein%%20names,genes,pathway,features,go,reviewed,existence,comments", jobID);
+			sprintf(queryString, "query=job:%s&format=tab&columns=entry%%20name,id,organism,protein%%20names,genes,pathway,features,go,reviewed,existence,comments,database(KEGG),database(GeneID),database(PATRIC),database(EnsemblBacteria)", jobID);
 			curl_easy_setopt(curlHandle, CURLOPT_URL, "http://www.uniprot.org/uniprot/");
 			curl_easy_setopt(curlHandle, CURLOPT_WRITEDATA, retBuffer);