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now can be asked to log at INFO level all concordant or discordant sites, or both 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@480 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-21 21:03:44 +00:00
parent 1f84b9647d
commit 5f37ba8f26
1 changed files with 32 additions and 22 deletions
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54
java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
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@ -17,6 +17,8 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
@Argument(fullName="consensus_cutoff", shortName="XC",required=true ) public Double CONS_CUTOFF;
@Argument(fullName="snp_cutoff", shortName="XS",required=true ) public Double SNP_CUTOFF;
@Argument(fullName="indel_cutoff", shortName="XI",required=true ) public Double INDEL_CUTOFF;
@Argument(fullName="log_concordant", shortName="LC",doc="If set, all trio-concordant sites will be logged at level INFO") public boolean LOG_CONCORDANT;
@Argument(fullName="log_discordant", shortName="LD",doc="If set, all trio-discordant sites will be logged at level INFO") public boolean LOG_DISCORDANT;
private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);
private final static String star = new String("*");
@ -91,23 +93,27 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
if ( mom_alleles.contains(kid_allele_1) && dad_alleles.contains(kid_allele_2) ||
mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
t.consistent_snp = 1;
// logger.info("consistent SNP at "+context.getLocation() +
// "("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " " +
// dad_alleles.get(0)+"/" +dad_alleles.get(1) + " " +
// kid_allele_1+"/" +kid_allele_2
// );
if ( LOG_CONCORDANT ) {
logger.info("consistent SNP at "+context.getLocation() +
"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " " +
dad_alleles.get(0)+"/" +dad_alleles.get(1) + " " +
kid_allele_1+"/" +kid_allele_2
);
}
} else {
// we are inconsistent. let's see what happened:
if ( kid.isSNP() && ! mom.isSNP() && ! dad.isSNP() ) t.missing_snp_in_parents = 1;
if ( ! kid.isSNP() && ( mom.isSNP() && mom.isHom() || dad.isSNP() && dad.isHom() ) ) t.missing_snp_in_kid = 1;
t.inconsistent_snp = 1;
logger.info("INconsistent SNP at "+context.getLocation() +
"("+ref+") mom:" + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " dad: " +
dad_alleles.get(0)+"/" +dad_alleles.get(1) + " kid: " +
kid_allele_1+"/" +kid_allele_2
);
if ( LOG_DISCORDANT ) {
logger.info("INconsistent SNP at "+context.getLocation() +
"("+ref+") mom:" + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " dad: " +
dad_alleles.get(0)+"/" +dad_alleles.get(1) + " kid: " +
kid_allele_1+"/" +kid_allele_2
);
}
}
return t;
}
@ -126,22 +132,26 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
t.consistent_indels = 1;
logger.info("consistent INDEL at "+context.getLocation() +
"("+ref+") mom:" + genotypeString(mom)+ " dad: " +
genotypeString(dad) + " kid: " +
genotypeString(kid)
);
if ( LOG_CONCORDANT ) {
logger.info("consistent INDEL at "+context.getLocation() +
"("+ref+") mom:" + genotypeString(mom)+ " dad: " +
genotypeString(dad) + " kid: " +
genotypeString(kid)
);
}
} else {
if ( kid.isIndel() && ! mom.isIndel() && ! dad.isIndel() ) t.missing_indels_in_parents = 1;
if ( ! kid.isIndel() && ( mom.isIndel() && mom.isHom() || dad.isIndel() && dad.isHom() ) ) t.missing_indels_in_kid = 1;
t.inconsistent_indels = 1;
logger.info("INconsistent INDEL at "+context.getLocation() +
"("+ref+") mom:" + genotypeString(mom)+ " dad: " +
genotypeString(dad) + " kid: " +
genotypeString(kid)
);
if ( LOG_DISCORDANT ) {
logger.info("INconsistent INDEL at "+context.getLocation() +
"("+ref+") mom:" + genotypeString(mom)+ " dad: " +
genotypeString(dad) + " kid: " +
genotypeString(kid)
);
}
}
return t;
}