Fix examples

Genomicsplc · Sep 5, 2018 · d9839ae · d9839ae
1 parent fdaeac7
commit d9839ae
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Showing 4 changed files with 18 additions and 18 deletions.
diff --git a/python/test/example.py b/python/test/example.py
@@ -263,7 +263,7 @@
 print(vk.decode_string_id(0xa850850492e77999))
 (b'A0A022YWF9', 10)
 
-print(vk.encode_string_num_id("ABC:0000123456", ":"))
+print(vk.encode_string_num_id("ABC:0000123456", ':'))
 # 15592178792074961472
 
 print(vk.decode_string_id(0xd8628c002001e240))

diff --git a/r/example/example.R b/r/example/example.R
@@ -216,19 +216,19 @@ MunmapBinfile(nrvk$MF)
 # Load the lookup table for rsID to VariantKey.
 # The input binary file can be generated using the resources/tools/rsvk.sh script.
 # This example uses the "c/test/data/rsvk.10.bin".
-rsvk <- MmapRSVKFile("../c/test/data/rsvk.10.bin", [4, 8])
-print(rsvknrows)
+rsvk <- MmapRSVKFile("../c/test/data/rsvk.10.bin", as.integer(c(4, 8)))
+print(rsvk$NROWS)
 # [1] 10
 
-x <- FindRvVariantKeyByRsid(rsvk$MC, 0, rsvknrows, rsid=0x00000061)
+x <- FindRvVariantKeyByRsid(rsvk$MC, 0, rsvk$NROWS, rsid=0x00000061)
 print(x)
 # $VK
 # [1] "80010274003a0000"
 #
 # $FIRST
 # [1] 3
 
-x <- GetNextRvVariantKeyByRsid(rsvk$MC, 2, rsvknrows, rsid=0x00000061)
+x <- GetNextRvVariantKeyByRsid(rsvk$MC, 2, rsvk$NROWS, rsid=0x00000061)
 print(x)
 # $VK
 # [1] "80010274003a0000"
@@ -244,9 +244,9 @@ MunmapBinfile(rsvk$MF)
 # Load the lookup table for rsID to VariantKey.
 # The input binary file can be generated using the resources/tools/rsvk.sh script.
 # This example uses the "c/test/data/rsvk.m.10.bin".
-rsvkm <- MmapRSVKFile("../c/test/data/rsvk.m.10.bin", [])
+rsvkm <- MmapRSVKFile("../c/test/data/rsvk.m.10.bin", as.integer(c()))
 
-x <- FindAllRvVariantKeyByRsid(rsvkm$MC, 0, rsvkmnrows, rsid=0x00000003)
+x <- FindAllRvVariantKeyByRsid(rsvkm$MC, 0, rsvkm$NROWS, rsid=0x00000003)
 print(x)
 # [[1]]
 # [1] "80010274003a0000"
@@ -265,17 +265,17 @@ MunmapBinfile(rsvkm$MF)
 # Load the lookup table for VariantKey ro rsID
 # The input binary file can be generated using the resources/tools/vkrs.sh script.
 # This example uses the "c/test/data/vkrs.10.bin".
-vkrs <- MmapVKRSFile("../c/test/data/vkrs.10.bin", [8, 4])
+vkrs <- MmapVKRSFile("../c/test/data/vkrs.10.bin", as.integer(c(8, 4)))
 
-x <- FindVrRsidByVariantKey(vkrs$MC, 0, vkrsnrows, vk="80010274003A0000")
+x <- FindVrRsidByVariantKey(vkrs$MC, 0, vkrs$NROWS, vk="80010274003A0000")
 print(x)
 # $RSID
 # [1] 97
 #
 # $FIRST
 # [1] 3
 
-x <- FindVrChromposRange(vkrs$MC, 0, vkrsnrows, chrom=0x14, pos_min=0x000256C5, pos_max=0x000256CB)
+x <- FindVrChromposRange(vkrs$MC, 0, vkrs$NROWS, chrom=0x14, pos_min=0x000256C5, pos_max=0x000256CB)
 print(x)
 #$RSID
 #[1] 9973
@@ -399,7 +399,7 @@ x <- DecodeStringID("a850850492e77999")
 print(x)
 # [1] "A0A022YWF9"
 
-x <- EncodeStringNumID("ABC:0000123456", ":")
+x <- EncodeStringNumID("ABC:0000123456", 58)
 print(x)
 # [1] "d8628c002001e240"
 

diff --git a/r/variantkey/src/variantkey.c b/r/variantkey/src/variantkey.c
@@ -244,11 +244,11 @@ SEXP R_mmap_rsvk_file(SEXP file, SEXP ctbytes)
     mmfile_t *mf = (mmfile_t *)Calloc(1, mmfile_t);
     rsidvar_cols_t *mc = (rsidvar_cols_t *)Calloc(1, rsidvar_cols_t);
     mf->ncols = (uint8_t)(LENGTH(ctbytes));
-    /*int *px = INTEGER(ctbytes);
+    int *px = INTEGER(ctbytes);
     for (int i = 0; i < mf->ncols; i++)
     {
         mf->ctbytes[i] = (uint8_t)px[i];
-    }*/
+    }
     mmap_rsvk_file(CHAR(STRING_ELT(file, 0)), mf, mc);
     SEXP emf = PROTECT(R_MakeExternalPtr(mf, R_NilValue, R_NilValue));
     R_RegisterCFinalizerEx(emf, destroy_mf, TRUE);
@@ -268,11 +268,11 @@ SEXP R_mmap_vkrs_file(SEXP file, SEXP ctbytes)
     mmfile_t *mf = (mmfile_t *)Calloc(1, mmfile_t);
     rsidvar_cols_t *mc = (rsidvar_cols_t *)Calloc(1, rsidvar_cols_t);
     mf->ncols = (uint8_t)(LENGTH(ctbytes));
-    /*int *px = INTEGER(ctbytes);
+    int *px = INTEGER(ctbytes);
     for (int i = 0; i < mf->ncols; i++)
     {
         mf->ctbytes[i] = (uint8_t)px[i];
-    }*/
+    }
     mmap_vkrs_file(CHAR(STRING_ELT(file, 0)), mf, mc);
     SEXP emf = PROTECT(R_MakeExternalPtr(mf, R_NilValue, R_NilValue));
     R_RegisterCFinalizerEx(emf, destroy_mf, TRUE);

diff --git a/r/variantkey/tests/testthat/test-rsidvar.R b/r/variantkey/tests/testthat/test-rsidvar.R
@@ -23,11 +23,11 @@ x <- rbind(
 colnames(x) <- list("item", "chrom", "pos", "refalt", "rsid", "vk")
 
 test_that("MmapRSVKFile", {
-    rsvk <<- MmapRSVKFile("../../../../c/test/data/rsvk.10.bin", c(4, 8))
+    rsvk <<- MmapRSVKFile("../../../../c/test/data/rsvk.10.bin", as.integer(c(4, 8)))
     expect_that(rsvk$NROWS, equals(10))
-    rsvkm <<- MmapRSVKFile("../../../../c/test/data/rsvk.m.10.bin", c())
+    rsvkm <<- MmapRSVKFile("../../../../c/test/data/rsvk.m.10.bin", as.integer(c()))
     expect_that(rsvkm$NROWS, equals(10))
-    vkrs <<- MmapVKRSFile("../../../../c/test/data/vkrs.10.bin", c(8, 4))
+    vkrs <<- MmapVKRSFile("../../../../c/test/data/vkrs.10.bin", as.integer(c(8, 4)))
     expect_that(vkrs$NROWS, equals(10))
 })