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YenaledYenaled
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Merge pull request #30 from pachterlab/lift
version bump 0.30.0 → 0.31.0
2 parents b8af2ab + 77ab439 commit da946a0

32 files changed

+2807
-153
lines changed

‎CMakeLists.txt‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -51,8 +51,9 @@ include(ExternalProject)
5151

5252

5353

54-
if (ZLIBNG)
54+
if (NOT ZLIBNG_DISABLE)
5555
message("zlib-ng enabled.")
56+
set(ZLIBNG "ON")
5657
ExternalProject_Add(zlib-ng
5758
PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng
5859
SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
@@ -61,7 +62,7 @@ if (ZLIBNG)
6162
BUILD_COMMAND cd zlib-ng && make
6263
INSTALL_COMMAND ""
6364
)
64-
endif(ZLIBNG)
65+
endif(ZLIBNG_DISABLE)
6566

6667

6768
if (USE_HTSLIB)

‎ext/htslib/bgzf.c‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -155,7 +155,7 @@ static int mode2level(const char *__restrict mode)
155155
BGZF *bgzf_open(const char *path, const char *mode)
156156
{
157157
BGZF *fp = 0;
158-
assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
158+
//assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
159159
if (strchr(mode, 'r')) {
160160
hFILE *fpr;
161161
if ((fpr = hopen(path, mode)) == 0) return 0;
@@ -177,7 +177,7 @@ BGZF *bgzf_open(const char *path, const char *mode)
177177
BGZF *bgzf_dopen(int fd, const char *mode)
178178
{
179179
BGZF *fp = 0;
180-
assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
180+
//assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
181181
if (strchr(mode, 'r')) {
182182
hFILE *fpr;
183183
if ((fpr = hdopen(fd, mode)) == 0) return 0;
@@ -199,7 +199,7 @@ BGZF *bgzf_dopen(int fd, const char *mode)
199199
BGZF *bgzf_hopen(hFILE *hfp, const char *mode)
200200
{
201201
BGZF *fp = NULL;
202-
assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
202+
//assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
203203
if (strchr(mode, 'r')) {
204204
fp = bgzf_read_init(hfp);
205205
if (fp == NULL) return NULL;

‎ext/htslib/faidx.c‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -171,14 +171,14 @@ void fai_destroy(faidx_t *fai)
171171
free(fai);
172172
}
173173

174-
int fai_build(const char *fn)
174+
int fai_build(const char *fn, const char* fai_file)
175175
{
176176
char *str;
177177
BGZF *bgzf;
178178
FILE *fp;
179179
faidx_t *fai;
180-
str = (char*)calloc(strlen(fn) + 5, 1);
181-
sprintf(str, "%s.fai", fn);
180+
str = (char*)calloc(strlen(fai_file) + 1, 1);
181+
sprintf(str, "%s", fai_file);
182182
bgzf = bgzf_open(fn, "r");
183183
if ( !bgzf ) {
184184
fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
@@ -243,13 +243,13 @@ FILE *download_and_open(const char *fn)
243243
}
244244
#endif
245245

246-
faidx_t *fai_load(const char *fn)
246+
faidx_t *fai_load(const char *fn, const char* fai_file)
247247
{
248248
char *str;
249249
FILE *fp;
250250
faidx_t *fai;
251-
str = (char*)calloc(strlen(fn) + 5, 1);
252-
sprintf(str, "%s.fai", fn);
251+
str = (char*)calloc(strlen(fai_file) + 1, 1);
252+
sprintf(str, "%s", fai_file);
253253

254254
#ifdef _USE_KNETFILE
255255
if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
@@ -267,7 +267,7 @@ faidx_t *fai_load(const char *fn)
267267
fp = fopen(str, "rb");
268268
if (fp == 0) {
269269
fprintf(stderr, "[fai_load] build FASTA index.\n");
270-
fai_build(fn);
270+
fai_build(fn, fai_file);
271271
fp = fopen(str, "rb");
272272
if (fp == 0) {
273273
fprintf(stderr, "[fai_load] fail to open FASTA index.\n");

‎ext/htslib/htslib/faidx.h‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -58,7 +58,7 @@ extern "C" {
5858
@return 0 on success; or -1 on failure
5959
@discussion File "fn.fai" will be generated.
6060
*/
61-
int fai_build(const char *fn);
61+
int fai_build(const char *fn, const char* fai_file);
6262

6363
/*!
6464
@abstract Distroy a faidx_t struct.
@@ -70,7 +70,7 @@ extern "C" {
7070
@abstract Load index from "fn.fai".
7171
@param fn File name of the FASTA file
7272
*/
73-
faidx_t *fai_load(const char *fn);
73+
faidx_t *fai_load(const char *fn, const char* fai_file);
7474

7575
/*!
7676
@abstract Fetch the sequence in a region.

‎func_tests/CMakeLists.txt‎

Lines changed: 58 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -38,3 +38,61 @@ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/b.fastq
3838

3939
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/configb.txt
4040
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
41+
42+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/test_1.vcf.gz
43+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
44+
45+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/test_2.vcf.gz
46+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
47+
48+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/vcf_validation.fa.gz
49+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
50+
51+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/example.SJ.tab
52+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
53+
54+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.1.R1.fa
55+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
56+
57+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.1.R1.fq
58+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
59+
60+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config.txt
61+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
62+
63+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_2.txt
64+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
65+
66+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.1.R2.fq
67+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
68+
69+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.2.R1.fq
70+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
71+
72+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.2.R2.fq
73+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
74+
75+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_3.txt
76+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
77+
78+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.3.R1.fq
79+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
80+
81+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.3.R2.fq
82+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
83+
84+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_4.txt
85+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
86+
87+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_5.txt
88+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
89+
90+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config_fastassign.txt
91+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
92+
93+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config_fastassign_2.txt
94+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
95+
96+
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/from_name.fq
97+
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
98+

‎func_tests/config_fastassign.txt‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
tags groups
2+
ATATATA A
3+
GTGTGTG B
4+
CCCCCC C
5+
AAAAAAAA D
6+
TTTTTTTT E
7+
GGGGGGG F

‎func_tests/config_fastassign_2.txt‎

Lines changed: 7 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,7 @@
1+
tags groups
2+
ATATATA A
3+
GTGTGTG B
4+
CCCCCC D
5+
AAAAAAAA D
6+
TTTTTTTT E
7+
GGGGGGG F

‎func_tests/example.SJ.tab‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
MT 3 5 +
2+
MT 3 5 +
3+
MT 2 5 -
4+
MT 31 60 +
5+
1 2 5 -
6+
1 3094999 3096284 +

‎func_tests/from_name.fq‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
@aaa 1:N:ATCCC+ATCG
2+
GGGGAGAGAGCGATAGACATA
3+
+
4+
JJJJJJJJJJJJJJJJJJJJJ

‎func_tests/nest.test.1.R1.fa‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
>a
2+
ATCGTTTCGCGCC

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