From 78409dca0d5896a0ab1ed63bb494921565c9fb56 Mon Sep 17 00:00:00 2001 From: aaron Date: Thu, 6 May 2010 16:36:58 +0000 Subject: [PATCH] turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a --- .../builders/TribbleRMDTrackBuilder.java | 11 +++++++++- .../sting/utils/genotype/vcf/VCFReader.java | 2 +- .../TribbleRMDTrackBuilderUnitTest.java | 20 +++++++++++++++--- settings/repository/org.broad/tribble-75.xml | 3 --- .../{tribble-75.jar => tribble-77.jar} | Bin 193121 -> 193446 bytes settings/repository/org.broad/tribble-77.xml | 3 +++ 6 files changed, 31 insertions(+), 8 deletions(-) delete mode 100644 settings/repository/org.broad/tribble-75.xml rename settings/repository/org.broad/{tribble-75.jar => tribble-77.jar} (93%) create mode 100644 settings/repository/org.broad/tribble-77.xml diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index 696b23534..f1a6d57c6 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java @@ -120,7 +120,16 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen */ public static LinearIndex createIndex(File inputFile, FeatureCodec codec) throws IOException { LinearIndexCreator create = new LinearIndexCreator(inputFile, codec); - return create.createIndex(); + create.setDisplayProgress(false); // don't display progress indicators + + // if we can write the index, we should, but if not just create it in memory + if (new File(inputFile.getAbsoluteFile() + linearIndexExtension).canWrite()) + return create.createIndex(); + else { + logger.info("Unable to write to location " + inputFile.getAbsoluteFile() + linearIndexExtension + " for index file, creating index in memory only"); + return create.createIndex(null); + } + } /** diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java index e65859284..5a22f8466 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java @@ -69,7 +69,7 @@ public class VCFReader implements Iterator, Iterable { } if (transform != null) codec.setTransformer(transform); try { - vcfReader = new FeatureReader(vcfFile,codec); + vcfReader = new FeatureReader(vcfFile,index,codec); iterator= vcfReader.iterator(); } catch (FileNotFoundException e) { throw new StingException("Unable to read VCF File from " + vcfFile, e); diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java index e1f1838c2..af39ecd98 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java @@ -23,10 +23,14 @@ package org.broadinstitute.sting.gatk.refdata.tracks.builders; +import org.broad.tribble.vcf.VCFCodec; import org.broadinstitute.sting.BaseTest; +import org.junit.Assert; import org.junit.Before; import org.junit.Test; +import java.io.File; +import java.io.IOException; import java.util.Map; @@ -49,9 +53,19 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest { @Test public void testBuilder() { Map classes = builder.getAvailableTrackNamesAndTypes(); - for (String c: classes.keySet()) { - System.err.println("class = " + c); + Assert.assertTrue(classes.size() > 0); + } + + @Test + public void testBuilderIndexUnwriteable() { + File vcfFile = new File(validationDataLocation + "/ROD_validation/mixedup.vcf"); + try { + builder.createIndex(vcfFile,new VCFCodec()); + } catch (IOException e) { + Assert.fail("Unable to make index because of IO exception " + e.getMessage()); } - //Assert.fail("Fail"); + // make sure we didn't write the file (check that it's length is zero) + Assert.assertEquals(0,new File(vcfFile + TribbleRMDTrackBuilder.linearIndexExtension).length()); + } } diff --git a/settings/repository/org.broad/tribble-75.xml b/settings/repository/org.broad/tribble-75.xml deleted file mode 100644 index e05fab800..000000000 --- a/settings/repository/org.broad/tribble-75.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/org.broad/tribble-75.jar b/settings/repository/org.broad/tribble-77.jar similarity index 93% rename from settings/repository/org.broad/tribble-75.jar rename to settings/repository/org.broad/tribble-77.jar index e8ee0024de91db9e7d7ed267b7f3054c9d9712ec..fcc69ef140db39e617be6bbf68511cf6fe248a67 100644 GIT binary patch delta 5147 zcmZu#3tUuH8vlQ1h8dW-z|6n^BPbyG07S$GxP!0WzQuNx(9H#dS`$}GEwcOVR;??v+FG=)uqcr(iIhIT&34A%`TZ)hq zw2>6JVkt5!FxfsYQi0#azh_rqL29u>0$)@1P(|o5?0%a9Pu{abIGHnS^y+uVWtjmv zl6^O_6Do7YOfc+inQ+1^W6;kXq$J;fDdtXL%aC^8*Ak|Tl@-*8FcuuPV*gX4KIgnX zx9K@AQjD*0X0)DuMp!Dh6@F!trYaZBeJNCd;3cKON_ox7?=%T~laD3&e%xmHsgreo zwui|;pPD|pad|kfJX}x67cngAs`S6PE?nu3-<_q5J-d5>s#4{xy@f`(3io*xr)=LY zivr^hK5uYN)MP4xqjrK(ll&viA(Fz83{srujy*0Us5mj+DD|ZJj~^c5Wgm!(He{kC1Q}Q= zAIs!pxfLsH2tuh9D{Zi%M7}&L(R0CgUd}H_%8OEVm5m>(t$4`>2VS;fjSViWmF!o7 zRA&K&R;;rj8opqxx0hf8HcA;?K3=u+>uYwrjyL3ElMS2krj&h4zHYIh3|m964dubu zF8%HZ#!ee{;cY8^8;o~sNXEM|fcK>L-BR)WVC)ITUMnhWsKf^{#C;~ z&7#}%o_1Os8D2PR{=DLXCvzT~`|x8$^XC(2+RoSQMCSd3VZM(CC3DGKlj~f1jgPgmDKjSM6U*njDuyAEDz@QY#Qvh44MBWJF_=21<~KzUZkUh%zh&BIwH@j#CkgXB9JhpP(X`$Wk(b z;T*4wAmo27TU6M+I~fgWPwOW}O9ECW8CK2z;HBu!5%#NwL*?a%b7D1Id1-z`c+Ey` zky$}eL6LCJ$+CuIg^<^7%G9b6ofjwBe#Ce~O_^aLGu)KvFlRbl9~B3JX6s}P&Jv-JlF;0DUxKN6F+zv_UNpO1#_aiCO;r47o zN(F8UtevYDub4Zc3cX!@72#&eq{>k6YV{_-Z8QwTY*667nNeUlL8}l&HTK zO^I#Jk400@lEl(j+Sz*1-7PcBNHZiV#O+)eWu3MDO=u}@ryu=FowW1EMT#BeE_yyQ z+7s%rN4ee6Zbuao)2fh`T89u%XlfPudqQO&nPgW}H?_{G(9n-Nyg%ZRjy`-SreHAA zFa!gTRl*(oGu}2{?wo9Hh2h-CBQcSWr^&p9@|pT;HuWfX{vzhAz<8|XzSzJLud>8u z+=m_b1>VL~RN#JmjA^LDbUrwKi3U7?3z&h+_!X|PrDhc11`6>{JWPaHq-s5q1A zobqz%A2OO|g(_4wg|2Ff`|?csG+y1Yx8C^cs&Xq(Zk2cJUh>A_@ULG^yRAy_?iXpH zTcMBMqVLuH-T!_$eQ202uA*zCxYPDiY5VOyLy_Dc(L)CFnL~8e@SFby&9o}NF`h*h z8-Jc{LB3aZ$LRUTDamjDnz{uk-M;lS&#urLP2@G))?cFS26yRS=zewW_c#2T1{z#P zE6p&tkD5hDn$lg8A$~My&t!=(m!hp1Bd%K%dL~Dd1*!U$Tzlu`T_J!RX{x>hZirZa z{!~#BqD0;KVs3ARo_kgV879}P5~1Tw{P&jr)(J6GGWAm@#7J3aJ+5A)D=@KM3{k9S z>&0+IsjC;c3M8BqV-=WlQcO~y=A@Wmuuh2w6j*vn|2qioQ}LEV)dBQqPHU7emdaCcUnwV{7a|BGzIQDBc>~`^^BOJg#Ude z5a!}0wlVjt=&Q)DpA|n>pyg~paCD=%S5ekA2IBZnqnN2E`R4)|zIRR(D2nsEcu;{S z&Wn2#s6EfIs**Kv2okWvI}KKon5cmBLIBLX5OB(tWA)<~0!6l76tk7!!i!?M`s1$S zuO|J>MUk5*H_^z7Cu2R_=yJ#_Xxp!RS!j3iB{rt&jyTfvm%bCKRrO8ZiCEL(+eqI# zg<`^U#*v6L8GmETD9=gm`vI=HlIy#Zcu)4b6j0B;!~*>X8|r%Fa0<~EUlIwb%9|yx zJgYPB+e^Zwa=0ORbH*rM51*seuK#8<+Z}P4?MlZJE;Ik+RK*`)kY(%rR+8%;Y%_UT z^iZDY3X@l_2#`muB$xj3ayB>VN+8S`Qeep{L%>%X8LV%*BI1;8wPgKmOFJt>uPq~w zp7fn?se&G^bUWud0XYV=Rg>rPWtX;hQfe$Ghl(?i!yopk`SPyqd`!xb+C{0{->wv< zAGylqka?ZG%0a9<(22EnKZWW8t_9+kEpGB0BK^ie@}zXEkzDa1xqG*H*pD0oyZD-L zNZ)czj7pGFZ;4|CTQoq9+qy_q)oi>j2C7^Ste-wCh8stY^e#fL9wmL5S#;C)9OXQh zTn`kd<9Gw#z&d{A%Wi!gP{{v=6=9eX_+UEW2GKV2Y*J?!E)LWWGivCfvh)~u2)mMGaJ2(J226YKyH1x^ei{uS! zg+-75UbvKa`l%TgKkf&}k=8~0?I02}dcq4LQg2`biq#@nRYTiZ z7QH_gP}$Z-q)gdm;ZvSRau?f&$99sh86#}^s+Pctyxt=1O*Z)R?h`S3Z4L+A(#CI< z{As!E{4iZEm4xsxKsR(lgW9+wh-+vRR4|iqMT0SF&`g8`%%Cx9TpnticEOm% zC`m^v$Iq#fzBq{r_M8 zR)5v4yXBho!ey&1Z@9r|fqXtbu=yQZvSA~2eO4JZP`M5y&u#+F?9iRG;HM#V;{A2c$5pN^I%$#9DodxmZBrn8L0Pz(w{q!KO#=U@n)V|40yjO93nEu; 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