Searched refs:scaffoldNames (Results 1 – 14 of 14) sorted by relevance
36 scaffoldNames.add(""); in SealRefInfo()111 return Tools.max(0, scaffoldNames.size()-1); in numScaffolds()118 if(scaffoldNames!=null && !scaffoldNames.isEmpty()){ in unloadScaffolds()119 scaffoldNames.clear(); in unloadScaffolds()120 scaffoldNames.trimToSize(); in unloadScaffolds()251 final ArrayList<String> scaffoldNames=new ArrayList<String>(); field in SealRefInfo
131 scaffoldNames.add(""); in Seal()701 ALLOW_LOCAL_ARRAYS=(scaffoldNames!=null && Tools.max(THREADS, 1)*3*8*scaffoldNames.size()<ram*5); in process2()806 if(scaffoldNames!=null && !scaffoldNames.isEmpty()){807 scaffoldNames.clear();808 scaffoldNames.trimToSize();1196 scaffoldNames.add(core);1217 id=scaffoldNames.size();1218 scaffoldNames.add(r1.id);1334 scaffoldNames.add("literal");1347 scaffoldNames.add(""+id);[all …]
920 ALLOW_LOCAL_ARRAYS=(scaffoldNames!=null && Tools.max(THREADS, 1)*3*8*scaffoldNames.size()<ram*5); in process2()1026 if(scaffoldNames!=null && !scaffoldNames.isEmpty()){ in unloadScaffolds()1027 scaffoldNames.clear(); in unloadScaffolds()1028 scaffoldNames.trimToSize(); in unloadScaffolds()1053 final String s=scaffoldNames.get(i); in writeStats()1112 final String s=scaffoldNames.get(i); in writeRPKM()1331 scaffoldNames.set(s, name); in toRefNames()1428 final Integer id=scaffoldNames.size(); in spawnLoadThreads()1431 scaffoldNames.add(id.toString()); in spawnLoadThreads()1997 final int alen=(scaffoldNames==null ? 0 : scaffoldNames.size()); in ProcessThread()[all …]
1138 scaffoldNames.clear(); in process2()1155 ALLOW_LOCAL_ARRAYS=(scaffoldNames!=null && Tools.max(THREADS, 1)*3*8*scaffoldNames.size()<ram*5); in process2()1406 if(scaffoldNames!=null && !scaffoldNames.isEmpty()){ in unloadScaffolds()1407 scaffoldNames.clear(); in unloadScaffolds()1408 scaffoldNames.trimToSize(); in unloadScaffolds()1433 final String s=scaffoldNames.get(i); in writeStats()1493 final String s=scaffoldNames.get(i); in writeRPKM()1701 scaffoldNames.set(s, name); in toRefNames()1805 scaffoldNames.add(id.toString()); in spawnLoadThreads()2410 final int alen=(scaffoldNames==null ? 0 : scaffoldNames.size()); in ProcessThread()[all …]
548 final byte[][][] names=Data.scaffoldNames; in loadScaffoldsFromIndex()
125 scaffoldNames=null; in processData()132 scaffoldNames=new ArrayList<String>(); in processData()204 if(scaffoldNames!=null){ in spawnLoadThreads()207 final Integer id=scaffoldNames.size(); in spawnLoadThreads()210 scaffoldNames.add(r1.id==null ? id.toString() : r1.id); in spawnLoadThreads()259 if(scaffoldNames!=null){ in spawnLoadThreads()260 final Integer id=scaffoldNames.size(); in spawnLoadThreads()263 scaffoldNames.add(id.toString()); in spawnLoadThreads()358 scaffoldNames.set(s, name); in toRefNames()722 public ArrayList<String> scaffoldNames; field in TableLoaderLockFree
60 scaffoldNames=null; in unloadAll()879 scaffoldNames=new byte[numChroms+1][][]; in setGenome2()948 for(int i=0; i<scaffoldNames.length; i++){ in setGenome2()962 scaffoldNames[chrom]=new byte[num][]; in setGenome2()997 scaffoldNames[chrom][x]=split[4].getBytes(); in setGenome2()1061 if(scaffoldNames[chrom]!=null){ in scafNameTable()1063 byte[] name=scaffoldNames[chrom][scafnum]; in scafNameTable()1174 if(scaffoldNames!=null){ in trimScaffoldNames()1175 for(int i=0; i<scaffoldNames.length; i++){ in trimScaffoldNames()1176 byte[][] matrix=scaffoldNames[i]; in trimScaffoldNames()[all …]
44 final byte[][] inames=Data.scaffoldNames[i]; in scaffolds()79 final byte[][] inames=Data.scaffoldNames[i]; in header1()111 final byte[][] inames=Data.scaffoldNames[i]; in printHeader1()159 final byte[][] inames=Data.scaffoldNames[chrom]; in printHeader1B()204 final byte[][] inames=Data.scaffoldNames[i]; in printHeader1()
46 name=Data.scaffoldNames[iChrom][scafIndex]; in setFromIndex()
111 byte[] name1=Data.scaffoldNames[bbchrom][bbscaffold]; in Header()194 final byte[] name1=Data.scaffoldNames[chrom1][idx1]; in customID_old()
377 name=Data.scaffoldNames[chrom][idx]; in getScaffoldName()
135 name1=Data.scaffoldNames[chrom1][idx1]; in SamLine()154 name2=Data.scaffoldNames[chrom2][idx2]; in SamLine()
3898 name=Data.scaffoldNames[chrom][idx]; in getScaffoldName()
456 final byte[][][] b3=Data.scaffoldNames; in getScaffoldAffixes()