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package stream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import dna.Data;
import fileIO.TextStreamWriter;
import shared.KillSwitch;
import shared.Shared;
import shared.Tools;
import structures.ByteBuilder;
/**
* @author Brian Bushnell
* @date Jul 7, 2014
*
*/
public class SamHeader {
public static ByteBuilder header0B(ByteBuilder bb){
// if(MAKE_TOPHAT_TAGS){
// return new ByteBuilder("@HD\tVN:"+(VERSION<1.4f ? "1.0" : "1.4")+"\tSO:unsorted");
// }
bb.append("@HD\tVN:");
bb.append((SamLine.VERSION<1.4f ? "1.3" : "1.4"));
bb.append("\tSO:unsorted");
return bb;
}
public static StringBuilder header0(){
// if(MAKE_TOPHAT_TAGS){
// return new StringBuilder("@HD\tVN:"+(SamLine.VERSION<1.4f ? "1.0" : "1.4")+"\tSO:unsorted");
// }
StringBuilder sb=new StringBuilder("@HD\tVN:"+(SamLine.VERSION<1.4f ? "1.3" : "1.4")+"\tSO:unsorted");
return sb;
}
static ArrayList<String> scaffolds(int minChrom, int maxChrom, boolean sort){
final ArrayList<String> list=new ArrayList<String>(4000);
final StringBuilder sb=new StringBuilder(1000);
for(int i=minChrom; i<=maxChrom && i<=Data.numChroms; i++){
final byte[][] inames=Data.scaffoldNames[i];
for(int j=0; j<Data.chromScaffolds[i]; j++){
final byte[] scn=inames[j];
sb.append("@SQ\tSN:");//+Data.scaffoldNames[i][j]);
if(scn==null){
assert(false) : "scaffoldName["+i+"]["+j+"] = null";
sb.append("null");
}else{
appendScafName(sb, scn);
}
sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j])));
// sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j]+1000L)));
// sb.append("\tAS:"+((Data.name==null ? "" : Data.name+" ")+"b"+Data.GENOME_BUILD).replace('\t', ' '));
sb.append('\n');
list.add(sb.toString());
sb.setLength(0);
}
}
if(sort){Shared.sort(list);}
return list;
}
public static StringBuilder header1(int minChrom, int maxChrom){
StringBuilder sb=new StringBuilder(20000);
if(SamLine.SORT_SCAFFOLDS){
ArrayList<String> scaffolds=scaffolds(minChrom, maxChrom, true);
for(int i=0; i<scaffolds.size(); i++){
sb.append(scaffolds.get(i));
scaffolds.set(i, null);
}
return sb;
}
for(int i=minChrom; i<=maxChrom && i<=Data.numChroms; i++){
final byte[][] inames=Data.scaffoldNames[i];
for(int j=0; j<Data.chromScaffolds[i]; j++){
byte[] scn=inames[j];
sb.append("@SQ\tSN:");//+Data.scaffoldNames[i][j]);
if(scn==null){
assert(false) : "scaffoldName["+i+"]["+j+"] = null";
sb.append("null");
}else{
appendScafName(sb, scn);
}
sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j])));
// sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j]+1000L)));
// sb.append("\tAS:"+((Data.name==null ? "" : Data.name+" ")+"build "+Data.GENOME_BUILD).replace('\t', ' '));
sb.append('\n');
}
}
return sb;
}
public static void printHeader1(int minChrom, int maxChrom, PrintWriter pw){
if(SamLine.SORT_SCAFFOLDS){
ArrayList<String> scaffolds=scaffolds(minChrom, maxChrom, true);
for(int i=0; i<scaffolds.size(); i++){
pw.print(scaffolds.set(i, null));
}
return;
}
for(int i=minChrom; i<=maxChrom && i<=Data.numChroms; i++){
final byte[][] inames=Data.scaffoldNames[i];
StringBuilder sb=new StringBuilder(256);
for(int j=0; j<Data.chromScaffolds[i]; j++){
final byte[] scn=inames[j];
// StringBuilder sb=new StringBuilder(7+(scn==null ? 4 : scn.length)+4+10+4+/*(Data.name==null ? 0 : Data.name.length()+1)+11*/+4);//last one could be 1
sb.append("@SQ\tSN:");//+Data.scaffoldNames[i][j]);
if(scn==null){
assert(false) : "scaffoldName["+i+"]["+j+"] = null";
sb.append("null");
}else{
appendScafName(sb, scn);
}
sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j])));
// sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j]+1000L)));
// sb.append("\tAS:"+((Data.name==null ? "" : Data.name+" ")+"b"+Data.GENOME_BUILD).replace('\t', ' '));
sb.append('\n');
pw.print(sb);
sb.setLength(0);
}
}
}
public static void printHeader1B(int minChrom, int maxChrom, ByteBuilder bb, OutputStream os){
if(verbose){System.err.println("printHeader1B("+minChrom+", "+maxChrom+")");}
if(SamLine.SORT_SCAFFOLDS){
if(verbose){System.err.println("Sorting scaffolds");}
ArrayList<String> scaffolds=scaffolds(minChrom, maxChrom, true);
for(int i=0; i<scaffolds.size(); i++){
String s=scaffolds.set(i, null);
bb.append(s);
if(bb.length>=32768){
try {
os.write(bb.array, 0, bb.length);
} catch (IOException e) {
KillSwitch.exceptionKill(e);
}
bb.setLength(0);
}
}
return;
}
if(verbose){System.err.println("Iterating over chroms");}
for(int chrom=minChrom; chrom<=maxChrom && chrom<=Data.numChroms; chrom++){
// if(verbose){System.err.println("chrom "+chrom);}
final byte[][] inames=Data.scaffoldNames[chrom];
// if(verbose){System.err.println("inames"+(inames==null ? " = null" : ".length = "+inames.length));}
final int numScafs=Data.chromScaffolds[chrom];
// if(verbose){System.err.println("scaffolds: "+numScafs);}
assert(inames.length==numScafs) : "Mismatch between number of scaffolds and names for chrom "+chrom+": "+inames.length+" != "+numScafs;
for(int scaf=0; scaf<numScafs; scaf++){
// if(verbose){System.err.println("chromScaffolds["+scaf+"] = "+(inames==null ? "=null" : ".length="+inames.length));}
final byte[] scafName=inames[scaf];
// if(verbose){System.err.println("scafName = "+(scafName==null ? "null" : new String(scafName)));}
bb.append("@SQ\tSN:");//+Data.scaffoldNames[i][j]);
if(scafName==null){
assert(false) : "scaffoldName["+chrom+"]["+scaf+"] = null";
bb.append(scafName);
}else{
appendScafName(bb, scafName);
}
bb.append("\tLN:");
bb.append(Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[chrom][scaf])));
// sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j]+1000L)));
// sb.append("\tAS:"+((Data.name==null ? "" : Data.name+" ")+"b"+Data.GENOME_BUILD).replace('\t', ' '));
bb.nl();
if(bb.length>=32768){
try {
os.write(bb.array, 0, bb.length);
} catch (IOException e) {
throw new RuntimeException(e);
}
bb.setLength(0);
}
}
}
}
public static void printHeader1(int minChrom, int maxChrom, TextStreamWriter tsw){
if(SamLine.SORT_SCAFFOLDS){
ArrayList<String> scaffolds=scaffolds(minChrom, maxChrom, true);
for(int i=0; i<scaffolds.size(); i++){
tsw.print(scaffolds.set(i, null));
}
return;
}
for(int i=minChrom; i<=maxChrom && i<=Data.numChroms; i++){
final byte[][] inames=Data.scaffoldNames[i];
final StringBuilder sb=new StringBuilder(256);
for(int j=0; j<Data.chromScaffolds[i]; j++){
final byte[] scn=inames[j];
// StringBuilder sb=new StringBuilder(7+(scn==null ? 4 : scn.length)+4+10+4+/*(Data.name==null ? 0 : Data.name.length()+1)+11*/+4);//last one could be 1
sb.append("@SQ\tSN:");//+Data.scaffoldNames[i][j]);
if(scn==null){
assert(false) : "scaffoldName["+i+"]["+j+"] = null";
sb.append("null");
}else{
appendScafName(sb, scn);
}
sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j])));
// sb.append("\tLN:"+Tools.min(Integer.MAX_VALUE, (Data.scaffoldLengths[i][j]+1000L)));
// sb.append("\tAS:"+((Data.name==null ? "" : Data.name+" ")+"b"+Data.GENOME_BUILD).replace('\t', ' '));
sb.append('\n');
tsw.print(sb);
sb.setLength(0);
}
}
}
static void appendScafName(StringBuilder sb, byte[] scn){
if(Data.scaffoldPrefixes){
int k=0;
while(k<scn.length && scn[k]!='$'){k++;}
k++;
while(k<scn.length){
sb.append((char)scn[k]);
k++;
}
}else{
final char[] buffer=Shared.getTLCB(scn.length);
for(int i=0; i<scn.length; i++){buffer[i]=(char)scn[i];}
sb.append(buffer, 0, scn.length);
}
}
static void appendScafName(ByteBuilder sb, byte[] scn){
if(Data.scaffoldPrefixes){
int k=0;
while(k<scn.length && scn[k]!='$'){k++;}
k++;
while(k<scn.length){
sb.append(scn[k]);
k++;
}
}else{
sb.append(scn);
}
}
public static StringBuilder header2(){
StringBuilder sb=new StringBuilder(1000);
// sb.append("@RG\tID:unknownRG\tSM:unknownSM\tPL:ILLUMINA\n"); //Can cause problems. If RG is in the header, reads may need extra fields.
// if(MAKE_TOPHAT_TAGS){
//// sb.append("@PG\tID:TopHat\tVN:2.0.6\tCL:/usr/common/jgi/aligners/tophat/2.0.6/bin/tophat -p 16 -r 0 --max-multihits 1 Creinhardtii_236 reads_1.fa reads_2.fa");
// sb.append("@PG\tID:TopHat\tVN:2.0.6");
// }else{
// sb.append("@PG\tID:BBMap\tPN:BBMap\tVN:"+Shared.BBMAP_VERSION_STRING);
// }
if(SamLine.READGROUP_ID!=null){
sb.append("@RG\tID:").append(SamLine.READGROUP_ID);
if(SamLine.READGROUP_CN!=null){sb.append("\tCN:").append(SamLine.READGROUP_CN);}
if(SamLine.READGROUP_DS!=null){sb.append("\tDS:").append(SamLine.READGROUP_DS);}
if(SamLine.READGROUP_DT!=null){sb.append("\tDT:").append(SamLine.READGROUP_DT);}
if(SamLine.READGROUP_FO!=null){sb.append("\tFO:").append(SamLine.READGROUP_FO);}
if(SamLine.READGROUP_KS!=null){sb.append("\tKS:").append(SamLine.READGROUP_KS);}
if(SamLine.READGROUP_LB!=null){sb.append("\tLB:").append(SamLine.READGROUP_LB);}
if(SamLine.READGROUP_PG!=null){sb.append("\tPG:").append(SamLine.READGROUP_PG);}
if(SamLine.READGROUP_PI!=null){sb.append("\tPI:").append(SamLine.READGROUP_PI);}
if(SamLine.READGROUP_PL!=null){sb.append("\tPL:").append(SamLine.READGROUP_PL);}
if(SamLine.READGROUP_PU!=null){sb.append("\tPU:").append(SamLine.READGROUP_PU);}
if(SamLine.READGROUP_SM!=null){sb.append("\tSM:").append(SamLine.READGROUP_SM);}
sb.append('\n');
}
sb.append("@PG\tID:BBMap\tPN:"+PN+"\tVN:");
sb.append(Shared.BBTOOLS_VERSION_STRING);
// assert(false) : sb+"\n"+PN;
if(Shared.BBMAP_CLASS!=null){
sb.append("\tCL:java");
{
List<String> list=null;
list=Shared.JVM_ARGS();
if(list!=null){
for(String s : list){
sb.append(' ');
sb.append(s);
}
}
}
sb.append(" align2."+Shared.BBMAP_CLASS);
if(Shared.COMMAND_LINE!=null){
for(String s : Shared.COMMAND_LINE){
sb.append(' ');
sb.append(s);
}
}
}
return sb;
}
public static ByteBuilder header2B(ByteBuilder sb){
if(SamLine.READGROUP_ID!=null){
sb.append("@RG\tID:").append(SamLine.READGROUP_ID);
if(SamLine.READGROUP_CN!=null){sb.append("\tCN:").append(SamLine.READGROUP_CN);}
if(SamLine.READGROUP_DS!=null){sb.append("\tDS:").append(SamLine.READGROUP_DS);}
if(SamLine.READGROUP_DT!=null){sb.append("\tDT:").append(SamLine.READGROUP_DT);}
if(SamLine.READGROUP_FO!=null){sb.append("\tFO:").append(SamLine.READGROUP_FO);}
if(SamLine.READGROUP_KS!=null){sb.append("\tKS:").append(SamLine.READGROUP_KS);}
if(SamLine.READGROUP_LB!=null){sb.append("\tLB:").append(SamLine.READGROUP_LB);}
if(SamLine.READGROUP_PG!=null){sb.append("\tPG:").append(SamLine.READGROUP_PG);}
if(SamLine.READGROUP_PI!=null){sb.append("\tPI:").append(SamLine.READGROUP_PI);}
if(SamLine.READGROUP_PL!=null){sb.append("\tPL:").append(SamLine.READGROUP_PL);}
if(SamLine.READGROUP_PU!=null){sb.append("\tPU:").append(SamLine.READGROUP_PU);}
if(SamLine.READGROUP_SM!=null){sb.append("\tSM:").append(SamLine.READGROUP_SM);}
sb.append('\n');
}
sb.append("@PG\tID:BBMap\tPN:"+PN+"\tVN:");
sb.append(Shared.BBTOOLS_VERSION_STRING);
// assert(false) : sb+"\n"+PN;
if(Shared.BBMAP_CLASS!=null){
sb.append("\tCL:java");
{
List<String> list=null;
list=Shared.JVM_ARGS();
if(list!=null){
for(String s : list){
sb.append(' ');
sb.append(s);
}
}
}
sb.append(" align2."+Shared.BBMAP_CLASS);
if(Shared.COMMAND_LINE!=null){
for(String s : Shared.COMMAND_LINE){
sb.append(' ');
sb.append(s);
}
}
}
return sb;
}
public static String PN="BBMap";
private static final boolean verbose=false;
}
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