Skip to content

Commit 59fba98

Browse files
eseilereseiler
committed
fix: new sharg version
1 parent a371785 commit 59fba98

File tree

7 files changed

+40
-13
lines changed

7 files changed

+40
-13
lines changed

‎cmake/package-lock.cmake‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,10 +31,11 @@ CPMDeclarePackage (seqan3
3131
)
3232

3333
# sharg
34-
set (NEEDLE_SHARG_VERSION 983dc3dc415d9fc193fb4dac110cc2ecac2ca4bc CACHE STRING "")
34+
set (NEEDLE_SHARG_VERSION 1.2.1 CACHE STRING "")
3535
CPMDeclarePackage (sharg
3636
NAME sharg
37-
GIT_TAG ${NEEDLE_SHARG_VERSION} # main
37+
VERSION ${NEEDLE_SHARG_VERSION}
38+
GIT_TAG ${NEEDLE_SHARG_VERSION}
3839
GITHUB_REPOSITORY seqan/sharg-parser
3940
SYSTEM TRUE
4041
EXCLUDE_FROM_ALL TRUE

‎test/cli/count_options_test.cpp‎

Lines changed: 15 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -12,17 +12,18 @@ struct count_options_test : public app_test
1212
TEST_F(count_options_test, no_options)
1313
{
1414
app_test_result result = execute_app("count");
15-
std::string expected{"needle-count - Get expression value depending on minimizers. "
16-
"This function is an alternative to pseudoaligners like kallisto. It "
17-
"estimates the expression value for all sequences in the genome file "
18-
"based on the exact minimiser occurrences of the given sequence files. "
19-
"Please run genome beforehand to create the genome file.\n"
20-
"======================================================================"
21-
"======================================================================"
22-
"======================================================================"
23-
"======================================================================"
24-
"==========================================\n "
25-
"Try -h or --help for more information.\n"};
15+
std::string expected{"needle-count - Get expression value depending on minimizers. This function is an alternative "
16+
"to pseudoaligners like kallisto. It estimates the expression value for all sequences in the "
17+
"genome file based on the exact minimiser occurrences of the given sequence files. Please run "
18+
"genome beforehand to create the genome "
19+
"file.\n======================================================================================"
20+
"============================================================================================="
21+
"============================================================================================="
22+
"==================================================\n"
23+
" needle count [-p|--paired] [-k|--kmer uint8] [-w|--window uint32] [--shape\n"
24+
" uint64] [--seed uint64] [-o|--out path] [-t|--threads uint16] --include\n"
25+
" path [--genome path] [--] path...\n"
26+
" Try -h or --help for more information.\n"};
2627
EXPECT_SUCCESS(result);
2728
EXPECT_EQ(result.out, expected);
2829
EXPECT_EQ(result.err, std::string{});
@@ -85,6 +86,9 @@ TEST_F(genome_options_test, no_options)
8586
app_test_result result = execute_app("genome");
8687
std::string expected{"needle-genome - Creates the genome file necessary as an input to count.\n"
8788
"=======================================================================\n"
89+
" needle genome [-k|--kmer uint8] [-w|--window uint32] [--shape uint64]\n"
90+
" [--seed uint64] [-o|--out path] [-t|--threads uint16] [--exclude path]\n"
91+
" [--] path\n"
8892
" Try -h or --help for more information.\n"};
8993
EXPECT_SUCCESS(result);
9094
EXPECT_EQ(result.out, expected);

‎test/cli/delete_options_test.cpp‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,8 @@ TEST_F(delete_options_test, delete_no_options)
1616
app_test_result result = execute_app("delete");
1717
std::string expected{"needle-delete - Delete experiments specified by their position from the Needle index.\n"
1818
"=====================================================================================\n"
19+
" needle delete [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
20+
" [-i|--in path] [--] uint64...\n"
1921
" Try -h or --help for more information.\n"};
2022
EXPECT_SUCCESS(result);
2123
EXPECT_EQ(result.out, expected);

‎test/cli/estimate_options_test.cpp‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,8 @@ TEST_F(estimate_options_test, no_options)
1616
app_test_result result = execute_app("estimate");
1717
std::string expected{"needle-estimate - Estimate expression value of transcript based on the Needle index.\n"
1818
"====================================================================================\n"
19+
" needle estimate [-m|--normalization-mode] [-i|--in path] [-o|--out path]\n"
20+
" [-t|--threads uint16] [-b|--batch uint64] [--] path\n"
1921
" Try -h or --help for more information.\n"};
2022
EXPECT_SUCCESS(result);
2123
EXPECT_EQ(result.out, expected);

‎test/cli/ibf_options_test.cpp‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,12 @@ TEST_F(ibf_options_test, ibf_no_options)
1414
app_test_result result = execute_app("ibf");
1515
std::string expected{"needle-ibf - Constructs the Needle index.\n"
1616
"=========================================\n"
17+
" needle ibf [-c|--compressed] [-p|--paired] [--ram] [-k|--kmer uint8]\n"
18+
" [-w|--window uint32] [--shape uint64] [--seed uint64] [-o|--out path]\n"
19+
" [-t|--threads uint16] [-f|--fpr double]... [-e|--expression_thresholds\n"
20+
" uint16]... [-l|--number_expression_thresholds uint8] [-n|--hash uint64]\n"
21+
" [--include path] [--exclude path] [--samples uint64]... [--cutoff\n"
22+
" uint8]... [--experiment-names bool] [--levels-by-genome path] [--] path...\n"
1723
" Try -h or --help for more information.\n"};
1824
EXPECT_SUCCESS(result);
1925
EXPECT_EQ(result.out, expected);
@@ -103,6 +109,10 @@ TEST_F(ibf_options_test, ibfmin_no_options)
103109
std::string expected{
104110
"needle-ibfmin - Constructs the Needle index from the minimiser files created by needle minimiser.\n"
105111
"=================================================================================================\n"
112+
" needle ibfmin [-c|--compressed] [-o|--out path] [-t|--threads uint16]\n"
113+
" [--levels-by-genome path] [-f|--fpr double]... [-e|--expression_thresholds\n"
114+
" uint16]... [-l|--number_expression_thresholds uint8] [-n|--hash uint64]\n"
115+
" [--] path...\n"
106116
" Try -h or --help for more information.\n"};
107117
EXPECT_SUCCESS(result);
108118
EXPECT_EQ(result.out, expected);

‎test/cli/insert_options_test.cpp‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,10 @@ TEST_F(insert_options_test, insert_no_options)
1616
app_test_result result = execute_app("insert");
1717
std::string expected{"needle-insert - Inserts into a given uncompressed Needle index.\n"
1818
"===============================================================\n"
19+
" needle insert [-p|--paired] [-c|--compressed] [--ram] [--include path]\n"
20+
" [--exclude path] [--samples uint64]... [--cutoff uint8]... [-t|--threads\n"
21+
" uint16] [-i|--in path] [--experiment-names bool] [--levels-by-genome path]\n"
22+
" [--] path...\n"
1923
" Try -h or --help for more information.\n"};
2024
EXPECT_SUCCESS(result);
2125
EXPECT_EQ(result.out, expected);

‎test/cli/minimiser_options_test.cpp‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,10 @@ TEST_F(minimiser_options_test, no_options)
1414
app_test_result result = execute_app("minimiser");
1515
std::string expected{"needle-minimiser - Calculates minimiser for given experiments.\n"
1616
"==============================================================\n"
17+
" needle minimiser [-p|--paired] [--ram] [-k|--kmer uint8] [-w|--window\n"
18+
" uint32] [--shape uint64] [--seed uint64] [-o|--out path] [-t|--threads\n"
19+
" uint16] [--include path] [--exclude path] [--samples uint64]... [--cutoff\n"
20+
" uint8]... [--] path...\n"
1721
" Try -h or --help for more information.\n"};
1822
EXPECT_SUCCESS(result);
1923
EXPECT_EQ(result.out, expected);

0 commit comments

Comments
 (0)