version bump 0.30.0 → 0.31.0

CMakeLists.txt

@@ -51,8 +51,9 @@ include(ExternalProject)
 
 
 
-if (ZLIBNG)
+if (NOT ZLIBNG_DISABLE)
     message("zlib-ng enabled.")
+    set(ZLIBNG "ON")
     ExternalProject_Add(zlib-ng
     PREFIX ${PROJECT_SOURCE_DIR}/ext/zlib-ng
     SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/zlib-ng
@@ -61,7 +62,7 @@ if (ZLIBNG)
     BUILD_COMMAND cd zlib-ng && make
     INSTALL_COMMAND ""
     )
-endif(ZLIBNG)
+endif(ZLIBNG_DISABLE)
 
 
 if (USE_HTSLIB)

ext/htslib/bgzf.c

@@ -155,7 +155,7 @@ static int mode2level(const char *__restrict mode)
 BGZF *bgzf_open(const char *path, const char *mode)
 {
 	BGZF *fp = 0;
-	assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+	//assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
 	if (strchr(mode, 'r')) {
 		hFILE *fpr;
 		if ((fpr = hopen(path, mode)) == 0) return 0;
@@ -177,7 +177,7 @@ BGZF *bgzf_open(const char *path, const char *mode)
 BGZF *bgzf_dopen(int fd, const char *mode)
 {
 	BGZF *fp = 0;
-	assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+	//assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
 	if (strchr(mode, 'r')) {
 		hFILE *fpr;
 		if ((fpr = hdopen(fd, mode)) == 0) return 0;
@@ -199,7 +199,7 @@ BGZF *bgzf_dopen(int fd, const char *mode)
 BGZF *bgzf_hopen(hFILE *hfp, const char *mode)
 {
 	BGZF *fp = NULL;
-	assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+	//assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
 	if (strchr(mode, 'r')) {
 		fp = bgzf_read_init(hfp);
 		if (fp == NULL) return NULL;

ext/htslib/faidx.c

@@ -171,14 +171,14 @@ void fai_destroy(faidx_t *fai)
 	free(fai);
 }
 
-int fai_build(const char *fn)
+int fai_build(const char *fn, const char* fai_file)
 {
 	char *str;
 	BGZF *bgzf;
 	FILE *fp;
 	faidx_t *fai;
-	str = (char*)calloc(strlen(fn) + 5, 1);
-	sprintf(str, "%s.fai", fn);
+	str = (char*)calloc(strlen(fai_file) + 1, 1);
+	sprintf(str, "%s", fai_file);
 	bgzf = bgzf_open(fn, "r");
 	if ( !bgzf ) {
 		fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
@@ -243,13 +243,13 @@ FILE *download_and_open(const char *fn)
 }
 #endif
 
-faidx_t *fai_load(const char *fn)
+faidx_t *fai_load(const char *fn, const char* fai_file)
 {
 	char *str;
 	FILE *fp;
 	faidx_t *fai;
-	str = (char*)calloc(strlen(fn) + 5, 1);
-	sprintf(str, "%s.fai", fn);
+	str = (char*)calloc(strlen(fai_file) + 1, 1);
+	sprintf(str, "%s", fai_file);
 
 #ifdef _USE_KNETFILE
     if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
@@ -267,7 +267,7 @@ faidx_t *fai_load(const char *fn)
         fp = fopen(str, "rb");
 	if (fp == 0) {
 		fprintf(stderr, "[fai_load] build FASTA index.\n");
-		fai_build(fn);
+		fai_build(fn, fai_file);
 		fp = fopen(str, "rb");
 		if (fp == 0) {
 			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");

ext/htslib/htslib/faidx.h

@@ -58,7 +58,7 @@ extern "C" {
 	  @return     0 on success; or -1 on failure
 	  @discussion File "fn.fai" will be generated.
 	 */
-	int fai_build(const char *fn);
+	int fai_build(const char *fn, const char* fai_file);
 
 	/*!
 	  @abstract    Distroy a faidx_t struct.
@@ -70,7 +70,7 @@ extern "C" {
 	  @abstract   Load index from "fn.fai".
 	  @param  fn  File name of the FASTA file
 	 */
-	faidx_t *fai_load(const char *fn);
+	faidx_t *fai_load(const char *fn, const char* fai_file);
 
 	/*!
 	  @abstract    Fetch the sequence in a region.

func_tests/CMakeLists.txt

@@ -38,3 +38,61 @@ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/b.fastq
 
 file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/configb.txt
      DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/test_1.vcf.gz
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/test_2.vcf.gz
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/vcf_validation.fa.gz
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/example.SJ.tab
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.1.R1.fa
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.1.R1.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_2.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.1.R2.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.2.R1.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.2.R2.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_3.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.3.R1.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest.test.3.R2.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_4.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/nest_config_5.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config_fastassign.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/config_fastassign_2.txt
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/from_name.fq
+     DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+

func_tests/config_fastassign.txt

@@ -0,0 +1,7 @@
+tags groups
+ATATATA A
+GTGTGTG B
+CCCCCC C
+AAAAAAAA D
+TTTTTTTT E
+GGGGGGG F

func_tests/config_fastassign_2.txt

@@ -0,0 +1,7 @@
+tags groups
+ATATATA A
+GTGTGTG B
+CCCCCC D
+AAAAAAAA D
+TTTTTTTT E
+GGGGGGG F

func_tests/example.SJ.tab

@@ -0,0 +1,6 @@
+MT	3 5	+
+MT	3 5	+
+MT      2 5     -
+MT	31 60   +
+1	2 5	-
+1	3094999 3096284 +

func_tests/from_name.fq

@@ -0,0 +1,4 @@
+@aaa 1:N:ATCCC+ATCG
+GGGGAGAGAGCGATAGACATA
++
+JJJJJJJJJJJJJJJJJJJJJ

func_tests/nest.test.1.R1.fa

@@ -0,0 +1,2 @@
+>a
+ATCGTTTCGCGCC

func_tests/nest.test.1.R1.fq

@@ -0,0 +1,4 @@
+@a
+ATCGTTTCGCGCG
++
+AAAAAAAAAAAAA

func_tests/nest.test.1.R2.fq

@@ -0,0 +1,4 @@
+@a
+CCCCCCCCCCCCC
++
+AAAAAAAAAAAAA

func_tests/nest.test.2.R1.fq

@@ -0,0 +1,8 @@
+@b
+CGCGAAAAAAAAAAAAA
++
+KKKKKKKKKKKKKKKKK
+@c
+ATCGTTTCGCGCG
++
+AAAAAAAAAAAAA

func_tests/nest.test.2.R2.fq

@@ -0,0 +1,8 @@
+@b
+ATCGGGAAAAAAAAAAA
++
+KKKKKKKKKKKKKKKKK
+@c
+ATCGTTTCGCGCG
++
+AAAAAAAAAAAAA

func_tests/nest.test.3.R1.fq

@@ -0,0 +1,16 @@
+@a
+GTGTGTGTCCCCCCCCTTTTTTTT
++
+KKKKKKKKKKKKKKKKKKKKKKKK
+@b
+GTGTGTGTAAAAAAAATTTTTTTT
++
+KKKKKKKKKKKKKKKKKKKKKKKK
+@c
+GTGTGTGTCCCCCCCCTTTTTTTT
++
+KKKKKKKKKKKKKKKKKKKKKKKK
+@d
+GTGTGTGTAAAAAAAATTTTTTTT
++
+KKKKKKKKKKKKKKKKKKKKKKKK

func_tests/nest.test.3.R2.fq

@@ -0,0 +1,16 @@
+@a
+AAAAAAAAGGGGGGGGG
++
+KKKKKKKKKKKKKKKKK
+@b
+AAAAAAAAGGGGGGGGG
++
+KKKKKKKKKKKKKKKKK
+@c
+ACCCCAAAGGGGGGGGG
++
+KKKKKKKKKKKKKKKKK
+@d
+ACCCCAAAGGGGGGGGG
++
+KKKKKKKKKKKKKKKKK

func_tests/nest_config.txt

@@ -0,0 +1,11 @@
+ids	tags	subs
+X	ATCG	GGGGG
+Y	CGCG
+Z	TTT
+
+@nest
+
+ids	tags	subs
+B	GTTT	AAA
+Y	CCCC
+Z	CGCGCG

func_tests/nest_config_2.txt

@@ -0,0 +1,15 @@
+@extract {X}<./func_tests/xxx[5]>
+
+ids	tags	subs
+X	ATCG	GGGGG
+Y	CGCG
+Z	TTT
+
+@nest
+
+ids	tags	subs
+B	GTTT	AAA
+Y	CCCC
+Z	CGCGCG
+
+

func_tests/nest_config_3.txt

@@ -0,0 +1,23 @@
+@extract {X}<xxx[5]>
+
+ids	tags	subs
+X	ATCG	GGGGG
+Y	CGCG
+Z	TTT
+
+@nest
+
+ids	tags	subs
+B	GTTT	AAA
+Y	CCCC
+Z	CGCGCG
+
+@nest
+
+@x-only
+@extract {GGA}<./func_tests/xx>1:-1
+
+tags	locations
+GGA	1
+
+

func_tests/nest_config_4.txt

@@ -0,0 +1,17 @@
+
+@assign
+
+@keep:
+R,R2
+
+ids	tags	locations
+R	AAAAAA	1:0:10
+R2	GGGGGG	1:10
+
+
+@nest
+
+@x-only
+@no-tags
+@filter-len 0,24,17
+

func_tests/nest_config_5.txt

@@ -0,0 +1,22 @@
+@extract {X}<xxx[5]>
+
+ids	tags	subs
+X	ATCG	GGGGG
+Y	CGCG
+Z	TTT
+
+@nest
+
+ids	tags	subs
+B	GTTT	AAA
+Y	CCCC
+Z	CGCGCG
+
+@nest
+
+@extract {GGA}<./func_tests/xx>1:-1
+
+tags	locations
+GGA	1
+
+