From 0c30a5ebc614cbeb377a50f0c7ff3af7a842b5c6 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 1 May 2013 15:25:23 -0400 Subject: [PATCH] Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VALUE) when converting from GL to integers. Increase capping to Integer.MAX_VALUE (2^31-1) which should be enough for reasonable sites now. Integration tests change because some tests have some hyper-deep pileups where this case was hit --- ...perGeneralPloidySuite2IntegrationTest.java | 6 +++--- ...GenotyperNormalCallingIntegrationTest.java | 4 ++-- ...lexAndSymbolicVariantsIntegrationTest.java | 4 ++-- .../HaplotypeCallerIntegrationTest.java | 2 +- ...nt-1.90.1442.jar => variant-1.90.1446.jar} | Bin 556173 -> 556173 bytes ...nt-1.90.1442.xml => variant-1.90.1446.xml} | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) rename settings/repository/org.broadinstitute/{variant-1.90.1442.jar => variant-1.90.1446.jar} (96%) rename settings/repository/org.broadinstitute/{variant-1.90.1442.xml => variant-1.90.1446.xml} (71%) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index e26822e07..ecc1ab66e 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -58,16 +58,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9f960977b1b8d90ac75ba4306336553c"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","5eabc12fc7b4f9749e6d1be0f5b45d14"); } @Test(enabled = true) public void testMT_SNP_DISCOVERY_sp4() { - executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","296917e690616682b79229ec5f923bdb"); + executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","71b7b9eac1e4a9b2b7e8c3689d1f29ec"); } @Test(enabled = true) public void testMT_SNP_GGA_sp10() { - executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "545d85ce79841f01886a5cf824a4a12c"); + executor.PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "fc36e925e269b035d4b27edb661be06b"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index 5734d670f..38ab8ee36 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, - Arrays.asList("21d1d3c6a50006c723cec738f19caeb6")); + Arrays.asList("1ab95513a3abb5b760578831c61ef94b")); executeTest("test Multiple SNP alleles", spec); } @@ -120,7 +120,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMismatchedPLs() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, - Arrays.asList("3011c20165951ca43c8a4e86a5835dbd")); + Arrays.asList("94bfccbd06043e90ae1b1c66fc3afe07")); executeTest("test mismatched PLs", spec); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index 90d7f493c..9d4c52798 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "5954a46971b7546d30151b068cded42a"); + "7d2cc5c4ece386beedf6b07dfbe5bf26"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "b3684c670f68f5a3a348a7fd2b25f10a"); + "a17856f709b546eaed486841d78248d2"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index 03d3e8a17..d5e163a88 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "65188ec4e3b91796f62bfb5b965ccf1f"); + "e2d32d0dce2c5502a8e877f6bbb65a10"); } @Test diff --git a/settings/repository/org.broadinstitute/variant-1.90.1442.jar b/settings/repository/org.broadinstitute/variant-1.90.1446.jar similarity index 96% rename from settings/repository/org.broadinstitute/variant-1.90.1442.jar rename to settings/repository/org.broadinstitute/variant-1.90.1446.jar index cf06f592eea3a230403c301e1d09305cdb76ebe9..9ca3c4f38aa4910227f0f704183965f3be8f1431 100644 GIT binary patch delta 3147 zcmYL~dr%eE9mntPp51c*d0fy7hN6&)LG1;uqGBKyxhRB(2=Y)K@)S_GJVjLS0VY$M z0*wUBLW;3AGeKi)RAN>lHMU04F(aX^#Bn+;zQV*dC=;nAW6lLE(r~Q9HHbPl9J2^>4MNqZih8WP9Lfre`Rr0Cb>#WPiAon(=HNKtcUJ zp6Kq5Z=FCH+5eEkz#9^G{;d6N7cgz=LDTB@eCC3ZGbnRY@eqcmjTpFM{re|g;1l?y znCEGII>aGk+8~3e>c`h)S9|sDUE^VXM5puX40#f&1rs3{Jhgl#lySN~OUT#TgR~{{ zgi8|8M1as11hh9nsDf72iBusHB;y954GK^PON6x`ky61U5Xie#5d49BPYRV#u-5vC zFcS`1`(vShF;L74qQAuK6&@VlcvP$K6AJ_-`kym1GncfHd7>gn`)6jfJM+a03&FoT zRy+-@X^BbV6z}b=cUp$0Y&$cho*t4-YC)Okq5WoqIEO*R``Mx?8tBe%#XUSr)}O`4 znB|&Cd9N8a#J|h}zs0x3Y6YnGA7YH6w^wI8t@xW|ozDKmtNM?n2-V}D&9ld8QvE8>Eb333c)ZX^m!bCNmNkKAYE{-DflOaYKt6InS4f^dwO{%RU3K@GRuO zk!$yD&iA>q-j_V(&TKxJfU~Mi`;!N*_G;C!V3Gu7hlG%Fo~d^kc_9F_fppT&1L8Bu zRVNsf<=FV>VcSi$KS^pKkzY}pI||*? zqYdO954g}mlKBam)lS0s9>w(#cYeOI2FNM6Pny$ZVw??2ton*bJT~esIqw15_md>k z6DWiF}3MgX(m7Fbc8+cgf>?HJ=mm z89s(DK9Ch2aqAEAcYLZh&dPUq=Hut(d``|6-(G1%Lf|!P)XrK z?s=@N;5&LFHzR?1>U8$Us1|-m13TSck~Qb&iZ`GA0$2JfFS=S!GkMY1yr~2qW9{Y& zD)Vp9XdLb2R%C{7Qy-MA+t~6@mXW&{cjpcFr zVp_T!N^b0?e{usd_fbz7a{at_!KlIZ%`i|k#FYlU74Gu(BI=}mw9_`&-+f5^DR_;f zdYLC}v!5iYd#UiE_N1TA;rqr0Xf!`1NmnTmz+3*tcHeD(D2Z|J<{|nLAN&Wy^dmmy z+!5NThrP8vij4ObbUOR<3XDp9^J_X=TXmlXao;TuXf1qTwcF2VlOJ@DIft#})RB@ju?MRU%*+fB7{y`%s-jpTz+e>11@K+X ziUC?yvuc3vRSI_I*eYXK9l*U9 zRu7Q12H{Hw#I0q!!E|{onqH1&<)HM%vTXofaV!U*)&au~FusbWRtJ3JfVg-p!x@)I!Xj|mJua_X!^?65MCWx!fj5?LX@q9g_vKMJKbd)508_`lTF?>)zKFGe>2MK7{j8X^fpW4K7hSxCy$Qd2$@YEWX0Lr^HI8~ooRsc#aoRncFep=ytpT=6c-IBlUO#q#X#`95B2C!&f!nT8A6hX2?9%fJZ%h zC;EK86E9iNF08P17t06dZ+D?7bvK5e*^O&?H?pnZbD$BA@l+!#1tqTu+quw$hi%Co GR`fs6;S~V@ delta 3147 zcmYL~c~Di?9mnr-?mLH_2l~KJ6cRB{En7r|KpyZ=2#W}^L>5^E1Rkr13NBzWO;eze zfVq%pY?_&%F*YhOR{}LQMA0!Lp{>MmGA(X#VjGl+)DknX_x#Rz%^!E}XTHDX{C>Z4 z&b?i8{#|qaE@{a!auft22&0w#-7aSQd1b$K=QkeRQJG>`clW%I6{`bFLRJNatq2PY z4PCb)A|%4k99v&+EAvaNEe%@g;^^Y|OO9bZ$JIqLeLV`2M=JY!%;G9|7mJZp9y}~s zM1U!&O?K54tF5>3xkxMskytIdEcy4OA-BPI4276_opN0o2j0IY(kLPdotv z9+V=0j)!9mvgS+*D78PothngTR=3`}VZKNZe0zc)glIuX3<6KBkcbtGE;);ZMjE6o zUnriFfu{Y%PBX1T+nprVVydar>0%TZ12>4BP=Gp8Cawi9R4%#)0C{zYq93^V920Ax zV6Ed5@kuyXyY7pF%fK4ox1L^jBx7ZrL@d&H!}qA5xsbNOwQ*gu&0E2m*Z)RpZBUr0V{v?4+%_ zBc&?f`|3TZxDV)G`{endu%i629LusNXmV2oXlEbD{Y=Y!C|lX=5C2zQ%joV;G6Fh1 zjiQ(osGvavo49q#-88KaWLlm1NnWFcI-(~s7(QD#m^+{w2AHAU6`f&AM0ucSmSv9# zSy>je@6g3ty7MjOZ1h17nKN00rbVc6&JW#op`=a)p%jpUgHaXBbZ`ZF${)0$Ow`2! z60^|-2P54^>$`U+59l|QJ}GK3QeIHodJxgdiqKI3;Od_{CS9 zE+9s2vKifE0mJPmm7O5xE)?zzNfP>z8#`Y)L+H2zXbz(&a2`;^*GOiu(KpZ;chG*E zLD?Qa8A!=s`Hs3NzO1QBo=O=z5upo|Q_#Ei?GoiIvkoj*&YK~&E>jta1`6s`?y}Xq zk18kG7{2^KF|dfMe^P#6Q@wmjxy~{lIinOZay+Z-XLM-P9`XK|g4u~ZF|O=YU_gtb zcK`gYerxHojt(eHZJSg~s-KM*wEb6=V{9?Yb)~}qMSVG?TwWUt1C769 zNMl3pzi(K@cJy+7Ruc9Q1o{N3#UJ8;9=B%|&GE6pi_Lzq3x1ImU1!AEtmungSY8Cl zudKof`vy%W;2vhRrQ*LKS9-L5^zEz)aS((M2lYk*Hmhx!*j??ofZep-3>*sIRPACu zj%Rn*Sc=P6Le`c({1;as%K-LJAlEYo7f+h>Z-xo0!7kYRM!3_PORkIFe>%+Z}B`W;ubbD-_5si1AJh$YmacNFLaPSpR8uq z{U&mcO>(ynIsLS({}4qY@qP-Ec+{Vh2z=yJ=VZM@>Qj?UvY?*x$)p%yX$pZ0pmwK_3h;TH z!Y5U{j+c669qIi4zf3Jj<%M5K&4T07HlHB z0QxqO?EoGHdyhUQd!hd8eLF)w_WdfzsN*@5I*)`c - +