{"action":"created","comment":{"url":"https://api.github.com/repos/magicDGS/thaplv/pulls/comments/81333905","pull_request_review_id":2321286,"id":81333905,"diff_hunk":"@@ -37,359 +37,367 @@\n  *\n  * Both variants could be in different chromosomes, but computations for them are not allowed yet\n  *\n- * @author Daniel Gómez-Sánchez\n+ * @author Daniel Gomez-Sanchez (magicDGS)\n+ * @deprecated should be implemented using AlleleVector or directly inside it\n  */\n+@Deprecated\n public class SNPpair {\n \n-\tprivate String referenceA;\n-\tprivate int positionA;\n-\tprivate String referenceB;\n-\tprivate int positionB;\n-\n-\t/**\n-\t * Counts for AB, Ab and ab, respectively\n-\t * ab can be computed with totalCounts-sum(counts)\n-\t */\n-\tprivate int[] counts;\n-\n-\t/**\n-\t * Total counts (without missing)\n-\t */\n-\tprivate int totalCounts;\n-\n-\t/**\n-\t * Constructor from one light-weight genotype and one variant from htsjdk\n-\t *\n-\t * @param genotype1\tthe first genotype\n-\t * @param variant2  the second genotype\n-\t */\n-\tpublic SNPpair(LightGenotype genotype1, VariantContext variant2) {\n-\t\tthis(genotype1, new LightGenotype(variant2));\n-\t}\n-\n-\t/**\n-\t * Constructor from two variant from htsjdk\n-\t *\n-\t * @param variant1\tthe first genotype\n-\t * @param variant2  the second genotype\n-\t */\n-\tpublic SNPpair(VariantContext variant1, VariantContext variant2) {\n-\t\tthis(new LightGenotype(variant1), variant2);\n-\t}\n-\n-\t/**\n-\t * Constructor from two light-weight genotypes\n-\t *\n-\t * @param genotype1\tthe first genotype\n-\t * @param genotype2  the second genotype\n-\t */\n-\tpublic SNPpair(LightGenotype genotype1, LightGenotype genotype2) {\n-\t\tif(genotype1.size() != genotype2.size()) {\n-\t\t\tthrow new IllegalArgumentException(\"Cannot initialize a SNPpair with genoptypes with differen lengths\");\n-\t\t}\n-\t\tint AB = 0;\n-\t\tint Ab = 0;\n-\t\tint aB = 0;\n-\t\ttotalCounts = 0;\n-\t\treferenceA = genotype1.getContig();\n-\t\tpositionA = genotype1.getPosition();\n-\t\treferenceB = genotype2.getContig();\n-\t\tpositionB = genotype2.getPosition();\n-\t\tfor(int i = 0; i < genotype1.size(); i++) {\n-\t\t\tLightGenotype.SNP snp1 = genotype1.getGenotypeAt(i);\n-\t\t\tLightGenotype.SNP snp2 = genotype2.getGenotypeAt(i);\n-\t\t\tif(snp1 == LightGenotype.SNP.N || snp2 == LightGenotype.SNP.N) {\n-\t\t\t\t// to don't store the total counts\n-\t\t\t\tcontinue;\n-\t\t\t} else if(snp1 == snp2) {\n-\t\t\t\tif(snp1 == LightGenotype.SNP.A) {\n-\t\t\t\t\tAB++;\n-\t\t\t\t}\n-\t\t\t} else {\n-\t\t\t\tif(snp1 == LightGenotype.SNP.A) {\n-\t\t\t\t\tAb++;\n-\t\t\t\t} else {\n-\t\t\t\t\taB++;\n-\t\t\t\t}\n-\t\t\t}\n-\t\t\ttotalCounts++;\n-\t\t}\n-\t\tcounts = new int[]{AB, Ab, aB};\n-\t\tpolarizeAlleles();\n-\t}\n-\n-\t/**\n-\t * Polarize alleles in terms of pA > pa and pB > pb\n-\t */\n-\tprivate void polarizeAlleles() {\n-\t\t// counts are in the order AB, Ab, aB\n-\t\tif(getMajorAC_A() < getMinorAC_A()) {\n-\t\t\t// change Ab <=> ab\n-\t\t\tcounts[1] = getCount_ab();\n-\t\t\t// change AB <=> aB\n-\t\t\tswap(0,2);\n-\t\t}\n-\t\tif(getMajorAC_B() < getMinorAC_B()) {\n-\t\t\t// change Ab <=> AB\n-\t\t\tswap(0, 1);\n-\t\t\t// chage ab <=> aB\n-\t\t\tcounts[2] = getCount_ab();\n-\t\t}\n-\t}\n-\n-\t/**\n-\t * Swap between two counts. Useful for polarize.\n-\t * Indexes are from 0 to 2 in the order: AB, Ab, aB\n-\t *\n-\t * @param index1 the first genotype to swap\n-\t * @param index2 the second genotype to swap\n-\t */\n-\tprivate void swap(int index1, int index2) {\n-\t\tint temp = counts[index1];\n-\t\tcounts[index1] = counts[index2];\n-\t\tcounts[index2] = temp;\n-\t}\n-\n-\t/**\n-\t * Check if at least one of the SNPs is a singleton\n-\t *\n-\t * @return true if A, B or both are singletons; false otherwise\n-\t */\n-\tpublic boolean oneIsSingleton() {\n-\t\treturn getMinorAC_A() == 1 || getMinorAC_B() == 1;\n-\t}\n-\n-\t/**\n-\t * Get the reference for the first variant (A)\n-\t *\n-\t * @return\tthe reference\n-\t */\n-\tpublic String getReferenceA() {\n-\t\treturn referenceA;\n-\t}\n-\n-\t/**\n-\t * Get the reference for the second variant (B)\n-\t *\n-\t * @return the reference\n-\t */\n-\tpublic String getReferenceB() {\n-\t\treturn referenceB;\n-\t}\n-\n-\t/**\n-\t * Get the position for the firs variant (A)\n-\t *\n-\t * @return the position\n-\t */\n-\tpublic int getPositionA() {\n-\t\treturn positionA;\n-\t}\n-\n-\t/**\n-\t * Get the position for the firs variant (B)\n-\t *\n-\t * @return the position\n-\t */\n-\tpublic int getPositionB() {\n-\t\treturn positionB;\n-\t}\n-\n-\t/**\n-\t * Get the distance between the two SNPs\n-\t * TODO: throw an error when they are in different chromosomes\n-\t *\n-\t * @return\tthe distance between the 2 SNPs\n-\t */\n-\tpublic int getDistance() {\n-\t\treturn Math.abs(positionA-positionB);\n-\t}\n-\n-\t/**\n-\t * Check if the first variant (A) is invariant\n-\t *\n-\t * @return\ttrue if is invariant; false otherwise\n-\t */\n-\tpublic boolean isInvariant_A() {\n-\t\treturn getMajorAC_A() == 0 || getMinorAC_A() == 0;\n-\t}\n-\n-\t/**\n-\t * Check if the second variant (B) is invariant\n-\t *\n-\t * @return true if is invariant; false otherwise\n-\t */\n-\tpublic boolean isInvariant_B() {\n-\t\treturn getMajorAC_B() == 0 || getMinorAC_B() == 0;\n-\t}\n-\n-\t/**\n-\t * Get the total counts\n-\t *\n-\t * @return\tthe number of available \"haplotypes\"\n-\t */\n-\tpublic int getTotalCounts() {\n-\t\treturn totalCounts;\n-\t}\n-\n-\t/**\n-\t * Get the major allele count for the first variant (A)\n-\t *\n-\t * @return\tthe major allele count\n-\t */\n-\tpublic int getMajorAC_A() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getCount_AB() + getCount_Ab();\n-\t}\n-\n-\t/**\n-\t * Get the major allele count for the second variant (B)\n-\t *\n-\t * @return\tthe major allele count\n-\t */\n-\tpublic int getMajorAC_B() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getCount_AB() + getCount_aB();\n-\t}\n-\n-\t/**\n-\t * Get the minor allele count for the first variant (A)\n-\t *\n-\t * @return\tthe minor allele count\n-\t */\n-\tpublic int getMinorAC_A() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getCount_aB() + getCount_ab();\n-\t}\n-\n-\t/**\n-\t * Get the minor allele count for the second variant (B)\n-\t *\n-\t * @return\tthe minor allele count\n-\t */\n-\tpublic int getMinorAC_B() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getCount_Ab() + getCount_ab();\n-\t}\n-\n-\t/**\n-\t * Get the major allele frequency for the first variant (A)\n-\t *\n-\t * @return\tthe major allele frequency\n-\t */\n-\tpublic double getMajorAF_A() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getMajorAC_A()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the major allele frequency for the second variant (B)\n-\t *\n-\t * @return\tthe major allele frequency\n-\t */\n-\tpublic double getMajorAF_B() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getMajorAC_B()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the minor allele frequency for the first variant (A)\n-\t *\n-\t * @return\tthe minor allele frequency\n-\t */\n-\tpublic double getMinorAF_A() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getMinorAC_A()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the minor allele frequency for the second variant (B)\n-\t *\n-\t * @return\tthe minor allele frequency\n-\t */\n-\tpublic double getMinorAF_B() {\n-\t\t// counts are in the order AB, Ab, aB, ab\n-\t\treturn getMinorAC_B()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the count for the \"haplotype\" AB\n-\t *\n-\t * @return the counts\n-\t */\n-\tpublic int getCount_AB() {\n-\t\treturn counts[0];\n-\t}\n-\n-\t/**\n-\t * Get the count for the \"haplotype\" ab\n-\t *\n-\t * @return the counts\n-\t */\n-\tpublic int getCount_ab() {\n-\t\treturn totalCounts - IntStream.of(counts).sum();\n-\t}\n-\n-\t/**\n-\t * Get the count for the \"haplotype\" Ab\n-\t *\n-\t * @return the counts\n-\t */\n-\tpublic int getCount_Ab() {\n-\t\treturn counts[1];\n-\t}\n-\n-\t/**\n-\t * Get the count for the \"haplotype\" ab\n-\t *\n-\t * @return the counts\n-\t */\n-\tpublic int getCount_aB() {\n-\t\treturn counts[2];\n-\t}\n-\n-\t/**\n-\t * Get the frequency for the \"haplotype\" AB\n-\t *\n-\t * @return the frequency\n-\t */\n-\tpublic double getFreq_AB() {\n-\t\treturn getCount_AB()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the frequency for the \"haplotype\" ab\n-\t *\n-\t * @return the frequency\n-\t */\n-\tpublic double getFreq_ab() {\n-\t\treturn getCount_ab()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the frequency for the \"haplotype\" Ab\n-\t *\n-\t * @return the frequency\n-\t */\n-\tpublic double getFreq_Ab() {\n-\t\treturn getCount_Ab()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Get the frequency for the \"haplotype\" aB\n-\t *\n-\t * @return the frequency\n-\t */\n-\tpublic double getFreq_aB() {\n-\t\treturn getCount_aB()/(double) getTotalCounts();\n-\t}\n-\n-\t/**\n-\t * Representation of the SNP pair with ref:position\n-\t *\n-\t * @return\trepresentation of the SNPpair\n-\t */\n-\tpublic String toString() {\n-\t\treturn String.format(\"%s:%s-%s:%s\", referenceA, positionA, referenceB, positionB);\n-\t}\n+    private String referenceA;\n+    private int positionA;\n+    private String referenceB;\n+    private int positionB;\n+\n+    /**\n+     * Counts for AB, Ab and ab, respectively\n+     * ab can be computed with totalCounts-sum(counts)\n+     */\n+    private int[] counts;\n+\n+    /**\n+     * Total counts (without missing)\n+     */\n+    private int totalCounts;","path":"src/main/java/org/magicdgs/thaplv/haplotypes/light/SNPpair.java","position":60,"original_position":376,"commit_id":"b737040d36e10ea8ce72776b1cfa636a327fd3c6","original_commit_id":"b737040d36e10ea8ce72776b1cfa636a327fd3c6","user":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars.githubusercontent.com/u/7352559?v=3","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"body":"No, it can't. Although it is effectively final, it uses the increment operation","created_at":"2016-09-30T13:02:43Z","updated_at":"2016-09-30T13:02:43Z","html_url":"https://github.com/magicDGS/thaplv/pull/33#discussion_r81333905","pull_request_url":"https://api.github.com/repos/magicDGS/thaplv/pulls/33","_links":{"self":{"href":"https://api.github.com/repos/magicDGS/thaplv/pulls/comments/81333905"},"html":{"href":"https://github.com/magicDGS/thaplv/pull/33#discussion_r81333905"},"pull_request":{"href":"https://api.github.com/repos/magicDGS/thaplv/pulls/33"}}},"pull_request":{"url":"https://api.github.com/repos/magicDGS/thaplv/pulls/33","id":86528674,"html_url":"https://github.com/magicDGS/thaplv/pull/33","diff_url":"https://github.com/magicDGS/thaplv/pull/33.diff","patch_url":"https://github.com/magicDGS/thaplv/pull/33.patch","issue_url":"https://api.github.com/repos/magicDGS/thaplv/issues/33","number":33,"state":"open","locked":false,"title":"WIP: LD components","user":{"login":"magicDGS","id":7352559,"avatar_url":"https://avatars.githubusercontent.com/u/7352559?v=3","gravatar_id":"","url":"https://api.github.com/users/magicDGS","html_url":"https://github.com/magicDGS","followers_url":"https://api.github.com/users/magicDGS/followers","following_url":"https://api.github.com/users/magicDGS/following{/other_user}","gists_url":"https://api.github.com/users/magicDGS/gists{/gist_id}","starred_url":"https://api.github.com/users/magicDGS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/magicDGS/subscriptions","organizations_url":"https://api.github.com/users/magicDGS/orgs","repos_url":"https://api.github.com/users/magicDGS/repos","events_url":"https://api.github.com/users/magicDGS/events{/privacy}","received_events_url":"https://api.github.com/users/magicDGS/received_events","type":"User","site_admin":false},"body":"This is a temporary solution for the LD decay tool, because it should be changed by a new and cleaner implementation.","created_at":"2016-09-23T15:03:45Z","updated_at":"2016-09-30T13:02:43Z","closed_at":null,"merged_at":null,"merge_commit_sha":"59336dccd24d54bf90ac4625228541be82d7d0e4","assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/magicDGS/thaplv/milestones/1","html_url":"https://github.com/magicDGS/thaplv/milestones/alpha","labels_url":"https://api.github.com/repos/magicDGS/thaplv/milestones/1/labels","id":1918058,"number":1,"title":"alpha","description":"* Migration from private repo.\r\n* Necessary refactoring for include in the GATK4 framework.\r\n* Integration tests for tools and unit tests for most functions in the 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