lots of new stuff, some generally useful, some one-off.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2673 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire
parent
78890c0bee
commit
877957761f
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@ -157,6 +157,37 @@ class VCFHomogenizer extends InputStream
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}
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}
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/////////
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// Info-level corrections
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String info = tokens[7];
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String new_info = "";
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String[] info_tokens = info.split(";");
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for (int i = 0; i < info_tokens.length; i++)
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{
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// Fix the case where AC includes the ref count first.
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if (info_tokens[i].startsWith("AC="))
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{
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String[] ACs = info_tokens[i].replaceAll("^AC=", "").split(",");
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if (ACs.length == alts.length+1)
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{
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String new_ACs = "";
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for (int j = 1; j < ACs.length; j++)
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{
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new_ACs += ACs[j];
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if (j != (ACs.length-1)) { new_ACs += ","; }
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}
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info_tokens[i] = "AC=" + new_ACs;
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}
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}
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new_info += info_tokens[i];
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if (i != (info_tokens.length-1)) { new_info += ";"; }
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}
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tokens[7] = new_info;
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/////////
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// Now put it back together and emit.
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String output = tokens[0];
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@ -66,11 +66,14 @@ class VCFSequenomAnalysis extends CommandLineProgram
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VCFRecord record1 = reader1.next();
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VCFRecord record2 = reader2.next();
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while(true)
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{
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if (record1 == null) { break; }
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if (record2 == null) { break; }
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String[] sample_names = record2.getSampleNames();
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Interval interval1 = VCFTool.getIntervalFromRecord(record1);
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Interval interval2 = VCFTool.getIntervalFromRecord(record2);
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@ -97,7 +100,7 @@ class VCFSequenomAnalysis extends CommandLineProgram
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int n_alt_sequenom = VCFTool.Compute_n_alt(record1);
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int n_alt_sequencing = VCFTool.Compute_n_alt(record2);
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double HWE_sequenom = VCFTool.Compute_HWE(record1);
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double HWE_sequenom = VCFTool.Compute_HWE(record1, sample_names);
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double HWE_sequencing = VCFTool.Compute_HWE(record2);
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boolean isPolymorphic_sequenom = (n_alt_sequenom > 0) ? true : false;
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.genotype.vcf.*;
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import edu.mit.broad.picard.util.Interval;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import java.io.*;
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@ -76,7 +77,6 @@ class VCFValidate extends CommandLineProgram
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class VCFStats extends CommandLineProgram
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{
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@Argument(fullName = "input", shortName = "input", doc = "file to read", required = true) public String in_filename;
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//@Argument(fullName = "output", shortName = "output", doc = "file to write", required = true) public String out_filename;
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@Argument(fullName = "auto_correct", shortName = "auto_correct", doc = "auto-correct the VCF file if it's off-spec", required = false) public Boolean autocorrect = false;
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@Argument(fullName = "locus", shortName = "locus", doc = "file listing loci to extract", required = true) public String locus_string;
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@ -102,25 +102,56 @@ class VCFStats extends CommandLineProgram
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// Stats collectors
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int transitions = 0;
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int transversions = 0;
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int dbsnp = 0;
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int total_snps = 0;
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int[] AC_histogram = new int[1000]; int highest_AC = 0;
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int[] AC_histogram = new int[1000]; int highest_AC = 0;
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int[] DP_histogram = new int[1000000]; int highest_DP = 0;
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int[] AC_transitions = new int[1000];
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int[] DP_transitions = new int[1000];
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int depth_sum = 0;
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boolean before = true;
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while(reader.hasNext())
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{
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VCFRecord record = reader.next();
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VCFRecord record = null;
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try
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{
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record = reader.next();
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}
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catch (Exception e)
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{
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System.err.printf("WARNING: %s\n", e.toString());
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continue;
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}
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Interval this_locus = VCFTool.getIntervalFromRecord(record);
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if (locus.intersects(this_locus))
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{
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before = false;
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Map<String,String> info = record.getInfoValues();
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int AC = Integer.parseInt(info.get("AC"));
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int AC = 0;
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int DP = 0;
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int DB = 0;
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if (info.containsKey("AC")) { AC = Integer.parseInt(info.get("AC")); }
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if (info.containsKey("DP")) { DP = Integer.parseInt(info.get("DP")); }
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if (info.containsKey("DB")) { DB = Integer.parseInt(info.get("DB")); }
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depth_sum += DP;
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dbsnp += DB; // 1 if in dbsnp, 0 otherwise
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AC_histogram[AC] += 1;
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if (AC > highest_AC) { highest_AC = AC; }
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if (VCFTool.isTransition(record)) { transitions += 1; }
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DP_histogram[DP] += 1;
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if (DP > highest_DP) { highest_DP = DP; }
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if (VCFTool.isTransition(record)) { transitions += 1; AC_transitions[AC] += 1; DP_transitions[DP] += 1; }
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else { transversions += 1; }
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total_snps += 1;
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@ -129,13 +160,49 @@ class VCFStats extends CommandLineProgram
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else if ((before == false) && (this_locus.compareTo(locus) > 0)) { break; }
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}
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System.out.printf("Total SNPs : %d\n", total_snps);
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System.out.printf("Ts/Tv : %.02f\n", (double)transitions / (double)transversions);
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double mean_depth = (double)depth_sum / (double)total_snps;
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double snp_rate = 1.0 / ((double)total_snps / (double)locus.length());
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int DP_running_sum = 0;
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int DP_1percent_low = -1;
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int DP_5percent_low = -1;
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for (int DP = 1; DP <= highest_DP; DP++)
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{
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if ((DP_1percent_low == -1) && (DP_running_sum >= 0.01*(double)total_snps)) { DP_1percent_low = DP; }
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if ((DP_5percent_low == -1) && (DP_running_sum >= 0.05*(double)total_snps)) { DP_5percent_low = DP; }
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DP_running_sum += DP_histogram[DP];
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}
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DP_running_sum = 0;
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int DP_1percent_high = -1;
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int DP_5percent_high = -1;
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for (int DP = highest_DP; DP >= 0; DP--)
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{
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if ((DP_1percent_high == -1) && (DP_running_sum >= 0.01*(double)total_snps)) { DP_1percent_high = DP; }
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if ((DP_5percent_high == -1) && (DP_running_sum >= 0.05*(double)total_snps)) { DP_5percent_high = DP; }
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DP_running_sum += DP_histogram[DP];
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}
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System.out.printf("Locus : %s\n", locus.toString());
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System.out.printf("Total SNPs : %d\n", total_snps);
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System.out.printf("SNP Rate : 1/%f\n", snp_rate);
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System.out.printf("Ts/Tv : %.02f\n", (double)transitions / (double)transversions);
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System.out.printf("%%dbsnp : %.02f\n", 100.0 * (double)dbsnp / (double)total_snps);
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System.out.printf("Average Depth : %f\n", mean_depth);
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System.out.printf("1%% Depth bounds : %d %d\n", DP_1percent_low, DP_1percent_high);
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System.out.printf("5%% Depth bounds : %d %d\n", DP_5percent_low, DP_5percent_high);
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System.out.printf("\n");
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System.out.printf("AAF\tCount\n");
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System.out.printf("table\tAAF\tCount\tTs/Tv\n");
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for (int AC = 1; AC <= highest_AC; AC++)
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{
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System.out.printf("%d\t%d\n", AC, AC_histogram[AC]);
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System.out.printf("AAF\t%d\t%d\t%f\n", AC, AC_histogram[AC], (double)AC_transitions[AC]/(double)(AC_histogram[AC]-AC_transitions[AC]));
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}
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System.out.printf("\n");
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System.out.printf("DEPTH\ttable\tDepth\tCount\tTs/Tv\n");
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for (int DP = 1; DP <= highest_DP; DP++)
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{
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System.out.printf("%d\t%d\t%f\n", DP, DP_histogram[DP], (double)DP_transitions[DP]/(double)(DP_histogram[DP]-DP_transitions[DP]));
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}
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System.out.printf("\n");
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@ -307,7 +374,6 @@ class FixRefFields extends CommandLineProgram
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}
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}
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class VCFGrep extends CommandLineProgram
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{
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@Argument(fullName = "input", shortName = "input", doc = "file to read", required = true) public String in_filename;
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@ -315,6 +381,58 @@ class VCFGrep extends CommandLineProgram
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@Argument(fullName = "auto_correct", shortName = "auto_correct", doc = "auto-correct the VCF file if it's off-spec", required = false) public Boolean autocorrect = false;
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@Argument(fullName = "loci", shortName = "loci", doc = "file listing loci to extract", required = true) public String loci_filename;
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@Override
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protected int execute()
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{
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HashSet<String> loci = new HashSet<String>();
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try
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{
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Scanner loci_reader = new Scanner(new File(loci_filename));
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while(loci_reader.hasNextLine())
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{
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String line = loci_reader.nextLine();
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line = line.replaceAll("\\s+", "");
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loci.add(line);
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}
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}
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catch (Exception e)
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{
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throw new RuntimeException(e);
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}
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try
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{
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PrintStream output = new PrintStream(new File(out_filename));
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Scanner reader = new Scanner(new File(in_filename));
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while(reader.hasNextLine())
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{
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String line = reader.nextLine();
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if (line.matches("^\\#.*$")) { output.print(line + "\n"); continue; }
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String[] tokens = line.split("\\s+");
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String locus = tokens[0] + ":" + tokens[1];
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if (loci.contains(locus)) { output.print(line + "\n"); continue; }
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}
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}
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catch (Exception e)
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{
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throw new RuntimeException(e);
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}
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return 0;
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}
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}
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class VCFGrep_old extends CommandLineProgram
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{
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@Argument(fullName = "input", shortName = "input", doc = "file to read", required = true) public String in_filename;
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@Argument(fullName = "output", shortName = "output", doc = "file to write", required = true) public String out_filename;
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@Argument(fullName = "auto_correct", shortName = "auto_correct", doc = "auto-correct the VCF file if it's off-spec", required = false) public Boolean autocorrect = false;
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@Argument(fullName = "loci", shortName = "loci", doc = "file listing loci to extract", required = true) public String loci_filename;
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@Override
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protected int execute()
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{
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@ -579,193 +697,6 @@ class VCFSimpleStats extends CommandLineProgram
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return 0;
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}
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}
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/*
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{
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@Argument(fullName = "vcf1", shortName = "vcf1", doc = "file to open", required = true) public String filename1;
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@Argument(fullName = "vcf2", shortName = "vcf2", doc = "file to open", required = true) public String filename2;
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@Argument(fullName = "out", shortName = "out", doc = "file to write results to", required = true) public String output_filename;
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@Argument(fullName = "auto_correct", shortName = "auto_correct", doc = "auto-correct the VCF file if it's off-spec", required = false) public Boolean autocorrect = false;
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@Argument(fullName = "verbose", shortName = "verbose", doc = "print extremely detailed stats", required = false) public Boolean verbose = false;
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@Override
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protected int execute()
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{
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//System.out.println("Loading " + filename + "...");
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PrintStream output = null;
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try
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{
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output = new PrintStream(new FileOutputStream(output_filename));
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}
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catch (Exception e)
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{
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throw new RuntimeException(e);
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}
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VCFReader reader1;
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VCFReader reader2;
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if (autocorrect)
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{
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reader1 = new VCFReader(VCFHomogenizer.create(filename1));
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reader2 = new VCFReader(VCFHomogenizer.create(filename2));
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}
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else
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{
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reader1 = new VCFReader(new File(filename1));
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reader2 = new VCFReader(new File(filename2));
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}
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VCFHeader header1 = reader1.getHeader();
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VCFHeader header2 = reader2.getHeader();
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VCFRecord record1 = reader1.next();
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VCFRecord record2 = reader2.next();
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int TP = 0;
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int FP = 0;
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int TN = 0;
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int FN = 0;
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int total = 0;
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while(true)
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{
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if (record1 == null) { break; }
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if (record2 == null) { break; }
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Interval interval1 = VCFTool.getIntervalFromRecord(record1);
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Interval interval2 = VCFTool.getIntervalFromRecord(record2);
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int comparison = interval1.compareTo(interval2);
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if (comparison == 0)
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{
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// records match! compute concordance.
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// (unless one of them is "filtered")
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if (record1.isFiltered() || record2.isFiltered())
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{
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record1 = reader1.next();
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record2 = reader2.next();
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}
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char ref = record1.getReferenceBase();
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String[] sample_names1 = record1.getSampleNames();
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String[] sample_names2 = record2.getSampleNames();
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List<VCFGenotypeRecord> genotypes1 = record1.getVCFGenotypeRecords();
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List<VCFGenotypeRecord> genotypes2 = record2.getVCFGenotypeRecords();
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Map<String, VCFGenotypeRecord> map2 = new HashMap<String, VCFGenotypeRecord>();
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for (int i = 0; i < genotypes2.size(); i++)
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{
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map2.put(genotypes2.get(i).getSampleName(), genotypes2.get(i));
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}
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long n_ref_1 = 0;
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long n_alt_1 = 0;
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long n_ref_2 = 0;
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long n_alt_2 = 0;
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for (int i = 0; i < sample_names1.length; i++)
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{
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VCFGenotypeRecord rec1 = genotypes1.get(i);
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VCFGenotypeRecord rec2 = map2.get(sample_names1[i]);
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if (rec2 == null) { continue; }
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Long gq1;
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if (rec1.getFields().get("GQ") != null)
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{
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Double gq1_double = Double.parseDouble(rec1.getFields().get("GQ"));
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gq1 = gq1_double.longValue();
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}
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else
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{
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gq1 = 0L;
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}
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List<VCFGenotypeEncoding> alleles1 = rec1.getAlleles();
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List<VCFGenotypeEncoding> alleles2 = rec2.getAlleles();
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String g1 = "";
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String g2 = "";
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for (int j = 0; j < alleles1.size(); j++) { g1 += alleles1.get(j).getBases(); }
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for (int j = 0; j < alleles2.size(); j++) { g2 += alleles2.get(j).getBases(); }
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char[] c1 = g1.toCharArray();
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char[] c2 = g2.toCharArray();
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Arrays.sort(c1);
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Arrays.sort(c2);
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g1 = new String(c1);
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g2 = new String(c2);
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if ((g1.equals("..")) ||
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(g2.equals("..")))
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{
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continue;
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}
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if (g1.charAt(0) == ref) { n_ref_1 += 1; } else { n_alt_1 += 1; }
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if (g1.charAt(1) == ref) { n_ref_1 += 1; } else { n_alt_1 += 1; }
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if (g2.charAt(0) == ref) { n_ref_2 += 1; } else { n_alt_2 += 1; }
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if (g2.charAt(1) == ref) { n_ref_2 += 1; } else { n_alt_2 += 1; }
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}
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if ((n_alt_1 > 0) && (n_alt_2 > 0)) { TP += 1; }
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if ((n_alt_1 > 0) && (n_alt_2 == 0)) { FP += 1; }
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if ((n_alt_1 == 0) && (n_alt_2 > 0)) { FN += 1; }
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if ((n_alt_1 == 0) && (n_alt_2 == 0)) { TN += 1; }
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total += 1;
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if (verbose)
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{
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output.printf("SNP "
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+ interval1.toString()
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+ " " + n_ref_1 + " " + n_alt_1
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+ " " + n_ref_2 + " " + n_alt_2 + "\n");
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}
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record1 = reader1.next();
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record2 = reader2.next();
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}
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else if (comparison > 0)
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{
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// interval1 is later than interval2.
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record2 = reader2.next();
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}
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else if (comparison < 0)
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{
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// interval2 is later than interval1.
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record1 = reader1.next();
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}
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}
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// Now output the statistics.
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output.printf("TP FP TN FN\n%d(%f) %d(%f) %d(%f) %d(%f)\n",
|
||||
TP, (double)TP/(double)total,
|
||||
FP, (double)FP/(double)total,
|
||||
TN, (double)TN/(double)total,
|
||||
FN, (double)FN/(double)total);
|
||||
|
||||
output.flush();
|
||||
output.close();
|
||||
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
*/
|
||||
|
||||
|
||||
class VCFConcordance extends CommandLineProgram
|
||||
|
|
@ -775,7 +706,9 @@ class VCFConcordance extends CommandLineProgram
|
|||
@Argument(fullName = "out", shortName = "out", doc = "file to write results to", required = true) public String output_filename;
|
||||
@Argument(fullName = "auto_correct", shortName = "auto_correct", doc = "auto-correct the VCF file if it's off-spec", required = false) public Boolean autocorrect = false;
|
||||
@Argument(fullName = "verbose", shortName = "verbose", doc = "print extremely detailed stats", required = false) public Boolean verbose = false;
|
||||
@Argument(fullName = "list_genotypes", shortName = "list_genotypes", doc = "print each person's genotype for debugging", required = false) public Boolean list_genotypes = false;
|
||||
@Argument(fullName = "qual_threshold", shortName = "qual_threshold", doc = "minimum genotype quality to consider", required = false) public long qual_threshold = 1;
|
||||
@Argument(fullName = "samples", shortName = "samples", doc = "optional list of individuals to score", required = false) public String samples_filename = null;
|
||||
|
||||
|
||||
@Override
|
||||
|
|
@ -792,7 +725,28 @@ class VCFConcordance extends CommandLineProgram
|
|||
|
||||
//
|
||||
/////////////////////////////////
|
||||
|
||||
|
||||
HashSet<String> sample_mask = new HashSet<String>();
|
||||
if (samples_filename != null)
|
||||
{
|
||||
Scanner samples_reader = null;
|
||||
try
|
||||
{
|
||||
samples_reader = new Scanner(new File(samples_filename));
|
||||
}
|
||||
catch (Exception e)
|
||||
{
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
while(samples_reader.hasNextLine())
|
||||
{
|
||||
String line = samples_reader.nextLine();
|
||||
line.replaceAll("^\\s+|\\s+$", "");
|
||||
sample_mask.add(line);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
PrintStream output = null;
|
||||
try
|
||||
{
|
||||
|
|
@ -833,6 +787,8 @@ class VCFConcordance extends CommandLineProgram
|
|||
Interval interval2 = VCFTool.getIntervalFromRecord(record2);
|
||||
|
||||
int comparison = interval1.compareTo(interval2);
|
||||
|
||||
//System.out.println("DBG: " + interval1 + " " + interval2);
|
||||
|
||||
if (comparison == 0)
|
||||
{
|
||||
|
|
@ -866,13 +822,19 @@ class VCFConcordance extends CommandLineProgram
|
|||
|
||||
for (int i = 0; i < sample_names1.length; i++)
|
||||
{
|
||||
if ((samples_filename != null) &&
|
||||
(! sample_mask.contains(sample_names1[i])))
|
||||
{
|
||||
continue;
|
||||
}
|
||||
|
||||
|
||||
VCFGenotypeRecord rec1 = genotypes1.get(i);
|
||||
VCFGenotypeRecord rec2 = map2.get(sample_names1[i]);
|
||||
|
||||
if (rec2 == null) { continue; }
|
||||
|
||||
Long gq1;
|
||||
|
||||
if (rec1.getFields().get("GQ") != null)
|
||||
{
|
||||
Double gq1_double = Double.parseDouble(rec1.getFields().get("GQ"));
|
||||
|
|
@ -883,6 +845,17 @@ class VCFConcordance extends CommandLineProgram
|
|||
gq1 = 0L;
|
||||
}
|
||||
|
||||
Long gq2;
|
||||
if (rec2.getFields().get("GQ") != null)
|
||||
{
|
||||
Double gq2_double = Double.parseDouble(rec2.getFields().get("GQ"));
|
||||
gq2 = gq2_double.longValue();
|
||||
}
|
||||
else
|
||||
{
|
||||
gq2 = 0L;
|
||||
}
|
||||
|
||||
List<VCFGenotypeEncoding> alleles1 = rec1.getAlleles();
|
||||
List<VCFGenotypeEncoding> alleles2 = rec2.getAlleles();
|
||||
|
||||
|
|
@ -901,6 +874,20 @@ class VCFConcordance extends CommandLineProgram
|
|||
g1 = new String(c1);
|
||||
g2 = new String(c2);
|
||||
|
||||
if (list_genotypes)
|
||||
{
|
||||
String flag = "";
|
||||
if (! g1.equals(g2)) { flag = "X"; }
|
||||
output.printf("GENOTYPES "
|
||||
+ interval1.toString()
|
||||
+ " " + sample_names1[i]
|
||||
+ " " + g1
|
||||
+ " " + g2
|
||||
+ " " + gq1
|
||||
+ " " + gq2
|
||||
+ " " + flag + "\n");
|
||||
}
|
||||
|
||||
if ((g1.equals("..")) ||
|
||||
(g2.equals("..")))
|
||||
{
|
||||
|
|
@ -917,18 +904,12 @@ class VCFConcordance extends CommandLineProgram
|
|||
Qual.get(gq1).add(ref, g1, g2);
|
||||
SNP.add(ref, g1, g2);
|
||||
|
||||
/*
|
||||
if (verbose)
|
||||
{
|
||||
String flag = "";
|
||||
if (! g1.equals(g2)) { flag = "X"; }
|
||||
output.printf("GENOTYPES " + interval1.toString() + " " + sample_names1[i] + " " + g1 + " " + g2 + " " + flag + "\n");
|
||||
}
|
||||
*/
|
||||
|
||||
}
|
||||
|
||||
if (verbose) { output.printf("SNP " + SNP.toString()); }
|
||||
if (verbose)
|
||||
{
|
||||
output.printf("SNP " + SNP.toString());
|
||||
}
|
||||
|
||||
if (! AAF.containsKey(n_alt)) { AAF.put(n_alt, new GenotypeConcordance(Long.toString(n_alt))); }
|
||||
AAF.get(n_alt).add(SNP);
|
||||
|
|
@ -1019,6 +1000,8 @@ public class VCFTool
|
|||
{
|
||||
public static void main(String args[])
|
||||
{
|
||||
SetupSequenceDictionary();
|
||||
|
||||
String mode = args[0];
|
||||
String[] realArgs = Arrays.copyOfRange(args, 1, args.length);
|
||||
|
||||
|
|
@ -1099,6 +1082,20 @@ public class VCFTool
|
|||
System.exit(0);
|
||||
}
|
||||
|
||||
if (mode.equals("optimize"))
|
||||
{
|
||||
VCFOptimize cm = new VCFOptimize();
|
||||
CommandLineProgram.start(cm,realArgs);
|
||||
System.exit(0);
|
||||
}
|
||||
|
||||
if (mode.equals("apply_cuts"))
|
||||
{
|
||||
VCFApplyCuts cm = new VCFApplyCuts();
|
||||
CommandLineProgram.start(cm,realArgs);
|
||||
System.exit(0);
|
||||
}
|
||||
|
||||
System.out.printf("ERROR: mode %s not defined.\n", mode);
|
||||
System.exit(-1);
|
||||
|
||||
|
|
@ -1107,7 +1104,22 @@ public class VCFTool
|
|||
|
||||
/////////////////////////
|
||||
// Some helpful utilities.
|
||||
|
||||
|
||||
// Total hack to set up a sequence dictionary for 1kG hg18/build36 without needing to load a fasta.
|
||||
public static SAMSequenceDictionary dict;
|
||||
public static void SetupSequenceDictionary()
|
||||
{
|
||||
dict = new SAMSequenceDictionary();
|
||||
for (int i = 1; i <= 22; i++)
|
||||
{
|
||||
dict.addSequence(new SAMSequenceRecord(String.format("%d", i)));
|
||||
}
|
||||
dict.addSequence(new SAMSequenceRecord("X"));
|
||||
dict.addSequence(new SAMSequenceRecord("Y"));
|
||||
dict.addSequence(new SAMSequenceRecord("M"));
|
||||
GenomeLocParser.setupRefContigOrdering(dict);
|
||||
}
|
||||
|
||||
public static Interval getIntervalFromRecord(VCFRecord record)
|
||||
{
|
||||
String chr = record.getLocation().getContig();
|
||||
|
|
|
|||
Loading…
Reference in New Issue