From ee1895c9584b5c1c1cef8547f9cc1795cbc2199c Mon Sep 17 00:00:00 2001 From: Toni Westbrook Date: Sun, 27 Mar 2016 22:52:28 -0400 Subject: [PATCH] Release/1.2.0 --- CHANGELOG.md | 5 +++++ bwa.c | 6 ++++-- main.h | 2 +- uniprot.c | 4 ++-- 4 files changed, 12 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 55e22b9..996ba78 100644 --- 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 index a791540..1dc810e 100644 --- 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 index 1e96730..24f8a3b 100644 --- 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 index de2f277..ef13b98 100644 --- 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);