From ad227819f5ced2042ad510a17a440d0c4dbb7aa3 Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Thu, 14 May 2020 11:31:12 -0400 Subject: [PATCH 1/3] remove r from argument --- build.gradle | 2 +- .../picard/sam/MarkDuplicates/optical_dupes.sam | 16 ---------------- .../sam/MarkDuplicates/optical_dupes_casava.sam | 16 ---------------- 3 files changed, 1 insertion(+), 33 deletions(-) delete mode 100644 testdata/picard/sam/MarkDuplicates/optical_dupes.sam delete mode 100644 testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam diff --git a/build.gradle b/build.gradle index 830004add1..446350103e 100644 --- a/build.gradle +++ b/build.gradle @@ -41,7 +41,7 @@ def looksLikeWereInAGitRepository(){ // Ensure that we have a clone of the git repository, and resolve any required git-lfs // resource files that are needed to run the build but are still lfs stub files. -def ensureBuildPrerequisites(rbuildPrerequisitesMessage) { +def ensureBuildPrerequisites(buildPrerequisitesMessage) { if (!JavaVersion.current().isJava8Compatible()) { throw new GradleException( "Java 8 or later is required to build Picard, but ${JavaVersion.current()} was found. " diff --git a/testdata/picard/sam/MarkDuplicates/optical_dupes.sam b/testdata/picard/sam/MarkDuplicates/optical_dupes.sam deleted file mode 100644 index 587c69a298..0000000000 --- a/testdata/picard/sam/MarkDuplicates/optical_dupes.sam +++ /dev/null @@ -1,16 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr2 LN:101 -@SQ SN:chr3 LN:101 -@SQ SN:chr4 LN:101 -@SQ SN:chr5 LN:101 -@SQ SN:chr6 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:1AAXX.1 SM:Hi,Mom! LB:mylib PL:ILLUMINA -@PG ID:MarkDuplicates PN:MarkDuplicates VN:1 CL:MarkDuplicates merge1.sam PP:bwa -@PG ID:bwa PN:bwa VN:1 CL:bwa aln -C4N4WACXX140821:8:1112:2344:1984 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates -C4N4WACXX140821:8:1112:2344:1985 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates -C4N4WACXX140821:8:1112:2344:1984 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates -C4N4WACXX140821:8:1112:2344:1985 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates diff --git a/testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam b/testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam deleted file mode 100644 index d135320876..0000000000 --- a/testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam +++ /dev/null @@ -1,16 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr2 LN:101 -@SQ SN:chr3 LN:101 -@SQ SN:chr4 LN:101 -@SQ SN:chr5 LN:101 -@SQ SN:chr6 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:1AAXX.1 SM:Hi,Mom! LB:mylib PL:ILLUMINA -@PG ID:MarkDuplicates PN:MarkDuplicates VN:1 CL:MarkDuplicates merge1.sam PP:bwa -@PG ID:bwa PN:bwa VN:1 CL:bwa aln -instr:run:C4N4WACXX140821:8:1112:2344:1984 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates -instr:run:C4N4WACXX140821:8:1112:2344:1985 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates -instr:run:C4N4WACXX140821:8:1112:2344:1984 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates -instr:run:C4N4WACXX140821:8:1112:2344:1985 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates From 3d253452fc9971678da3f1ef8d7ae7bd2ecee3f9 Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Thu, 14 May 2020 13:56:47 -0400 Subject: [PATCH 2/3] Revert "remove r from argument" This reverts commit ad227819f5ced2042ad510a17a440d0c4dbb7aa3. --- build.gradle | 2 +- .../picard/sam/MarkDuplicates/optical_dupes.sam | 16 ++++++++++++++++ .../sam/MarkDuplicates/optical_dupes_casava.sam | 16 ++++++++++++++++ 3 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 testdata/picard/sam/MarkDuplicates/optical_dupes.sam create mode 100644 testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam diff --git a/build.gradle b/build.gradle index 446350103e..830004add1 100644 --- a/build.gradle +++ b/build.gradle @@ -41,7 +41,7 @@ def looksLikeWereInAGitRepository(){ // Ensure that we have a clone of the git repository, and resolve any required git-lfs // resource files that are needed to run the build but are still lfs stub files. -def ensureBuildPrerequisites(buildPrerequisitesMessage) { +def ensureBuildPrerequisites(rbuildPrerequisitesMessage) { if (!JavaVersion.current().isJava8Compatible()) { throw new GradleException( "Java 8 or later is required to build Picard, but ${JavaVersion.current()} was found. " diff --git a/testdata/picard/sam/MarkDuplicates/optical_dupes.sam b/testdata/picard/sam/MarkDuplicates/optical_dupes.sam new file mode 100644 index 0000000000..587c69a298 --- /dev/null +++ b/testdata/picard/sam/MarkDuplicates/optical_dupes.sam @@ -0,0 +1,16 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr2 LN:101 +@SQ SN:chr3 LN:101 +@SQ SN:chr4 LN:101 +@SQ SN:chr5 LN:101 +@SQ SN:chr6 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:1AAXX.1 SM:Hi,Mom! LB:mylib PL:ILLUMINA +@PG ID:MarkDuplicates PN:MarkDuplicates VN:1 CL:MarkDuplicates merge1.sam PP:bwa +@PG ID:bwa PN:bwa VN:1 CL:bwa aln +C4N4WACXX140821:8:1112:2344:1984 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates +C4N4WACXX140821:8:1112:2344:1985 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates +C4N4WACXX140821:8:1112:2344:1984 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates +C4N4WACXX140821:8:1112:2344:1985 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates diff --git a/testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam b/testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam new file mode 100644 index 0000000000..d135320876 --- /dev/null +++ b/testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam @@ -0,0 +1,16 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr2 LN:101 +@SQ SN:chr3 LN:101 +@SQ SN:chr4 LN:101 +@SQ SN:chr5 LN:101 +@SQ SN:chr6 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:1AAXX.1 SM:Hi,Mom! LB:mylib PL:ILLUMINA +@PG ID:MarkDuplicates PN:MarkDuplicates VN:1 CL:MarkDuplicates merge1.sam PP:bwa +@PG ID:bwa PN:bwa VN:1 CL:bwa aln +instr:run:C4N4WACXX140821:8:1112:2344:1984 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates +instr:run:C4N4WACXX140821:8:1112:2344:1985 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1AAXX.1 PG:Z:MarkDuplicates +instr:run:C4N4WACXX140821:8:1112:2344:1984 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates +instr:run:C4N4WACXX140821:8:1112:2344:1985 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:1AAXX.1 PG:Z:MarkDuplicates From 11ebdee558936beb7b04e6dc0b48e83ccc897d95 Mon Sep 17 00:00:00 2001 From: nikellepetrillo Date: Thu, 14 May 2020 14:00:37 -0400 Subject: [PATCH 3/3] include accidentally deleted test files --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 830004add1..446350103e 100644 --- a/build.gradle +++ b/build.gradle @@ -41,7 +41,7 @@ def looksLikeWereInAGitRepository(){ // Ensure that we have a clone of the git repository, and resolve any required git-lfs // resource files that are needed to run the build but are still lfs stub files. -def ensureBuildPrerequisites(rbuildPrerequisitesMessage) { +def ensureBuildPrerequisites(buildPrerequisitesMessage) { if (!JavaVersion.current().isJava8Compatible()) { throw new GradleException( "Java 8 or later is required to build Picard, but ${JavaVersion.current()} was found. "