bio-bigwig 0.0.1 → 0.0.3

data/ext/bio/bigwig/libBigWig/io.c

@@ -12,7 +12,7 @@
 size_t GLOBAL_DEFAULTBUFFERSIZE;
 
 #ifndef NOCURL
-uint64_t getContentLength(URL_t *URL) {
+uint64_t getContentLength(const URL_t *URL) {
     double size;
     if(curl_easy_getinfo(URL->x.curl, CURLINFO_CONTENT_LENGTH_DOWNLOAD, &size) != CURLE_OK) {
         return 0;
@@ -98,7 +98,7 @@ size_t urlRead(URL_t *URL, void *buf, size_t bufSize) {
 #endif
 }
 
-size_t bwFillBuffer(void *inBuf, size_t l, size_t nmemb, void *pURL) {
+size_t bwFillBuffer(const void *inBuf, size_t l, size_t nmemb, void *pURL) {
     URL_t *URL = (URL_t*) pURL;
     void *p = URL->memBuf;
     size_t copied = l*nmemb;
@@ -158,7 +158,7 @@ CURLcode urlSeek(URL_t *URL, size_t pos) {
 #endif
 }
 
-URL_t *urlOpen(char *fname, CURLcode (*callBack)(CURL*), const char *mode) {
+URL_t *urlOpen(const char *fname, CURLcode (*callBack)(CURL*), const char *mode) {
     URL_t *URL = calloc(1, sizeof(URL_t));
     if(!URL) return NULL;
     char *url = NULL, *req = NULL;

data/lib/bio/bigwig/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class BigWig
-    VERSION = "0.0.1"
+    VERSION = "0.0.3"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigwig
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.3
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-01-30 00:00:00.000000000 Z
+date: 2024-09-20 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for libBigWig (https://github.com/dpryan79/libBigWig),
   which provides high-speed access to bigWig or bigBed files.
@@ -34,16 +34,9 @@ files:
 - ext/bio/bigwig/libBigWig/bwValues.h
 - ext/bio/bigwig/libBigWig/bwWrite.c
 - ext/bio/bigwig/libBigWig/io.c
-- ext/bio/bigwig/libBigWig/test/exampleWrite.c
-- ext/bio/bigwig/libBigWig/test/testBigBed.c
-- ext/bio/bigwig/libBigWig/test/testIterator.c
-- ext/bio/bigwig/libBigWig/test/testLocal.c
-- ext/bio/bigwig/libBigWig/test/testRemote.c
-- ext/bio/bigwig/libBigWig/test/testRemoteManyContigs.c
-- ext/bio/bigwig/libBigWig/test/testWrite.c
 - lib/bio/bigwig.rb
 - lib/bio/bigwig/version.rb
-homepage: https://github.com/kojix2/bw-ruby
+homepage: https://github.com/kojix2/bio-bigwig
 licenses:
 - MIT
 metadata: {}
@@ -62,7 +55,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.3
+rubygems_version: 3.4.19
 signing_key: 
 specification_version: 4
 summary: A ruby library for accessing bigWig / bigBed files

data/ext/bio/bigwig/libBigWig/test/exampleWrite.c

@@ -1,76 +0,0 @@
-#include "bigWig.h"
-
-int main(int argc, char *argv[]) {
-    bigWigFile_t *fp = NULL;
-    char *chroms[] = {"1", "2"};
-    char *chromsUse[] = {"1", "1", "1"};
-    uint32_t chrLens[] = {1000000, 1500000};
-    uint32_t starts[] = {0, 100, 125,
-                         200, 220, 230,
-                         500, 600, 625,
-                         700, 800, 850};
-    uint32_t ends[] = {5, 120, 126,
-                       205, 226, 231};
-    float values[] = {0.0f, 1.0f, 200.0f,
-                      -2.0f, 150.0f, 25.0f,
-                      0.0f, 1.0f, 200.0f,
-                      -2.0f, 150.0f, 25.0f,
-                      -5.0f, -20.0f, 25.0f,
-                      -5.0f, -20.0f, 25.0f};
-    
-
-    if(bwInit(1<<17) != 0) {
-        fprintf(stderr, "Received an error in bwInit\n");
-        return 1;
-    }
-
-    fp = bwOpen("test/example_output.bw", NULL, "w");
-    if(!fp) {
-        fprintf(stderr, "An error occurred while opening example_output.bw for writingn\n");
-        return 1;
-    }
-
-    //Allow up to 10 zoom levels, though fewer will be used in practice
-    if(bwCreateHdr(fp, 10)) goto error;
-
-    //Create the chromosome lists
-    fp->cl = bwCreateChromList(chroms, chrLens, 2);
-    if(!fp->cl) goto error;
-
-    //Write the header
-    if(bwWriteHdr(fp)) goto error;
-
-    //Some example bedGraph-like entries
-    if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
-    //We can continue appending similarly formatted entries
-    //N.B. you can't append a different chromosome (those always go into different
-    if(bwAppendIntervals(fp, starts+3, ends+3, values+3, 3)) goto error;
-
-    //Add a new block of entries with a span. Since bwAdd/AppendIntervals was just used we MUST create a new block
-    if(bwAddIntervalSpans(fp, "1", starts+6, 20, values+6, 3)) goto error;
-    //We can continue appending similarly formatted entries
-    if(bwAppendIntervalSpans(fp, starts+9, values+9, 3)) goto error;
-
-    //Add a new block of fixed-step entries
-    if(bwAddIntervalSpanSteps(fp, "1", 900, 20, 30, values+12, 3)) goto error;
-    //The start is then 760, since that's where the previous step ended
-    if(bwAppendIntervalSpanSteps(fp, values+15, 3)) goto error;
-
-    //Add a new chromosome
-    chromsUse[0] = "2";
-    chromsUse[1] = "2";
-    chromsUse[2] = "2";
-    if(bwAddIntervals(fp, chromsUse, starts, ends, values, 3)) goto error;
-
-    //Closing the file causes the zoom levels to be created
-    bwClose(fp);
-    bwCleanup();
-
-    return 0;
-
-error:
-    fprintf(stderr, "Received an error somewhere!\n");
-    bwClose(fp);
-    bwCleanup();
-    return 1;
-}

data/ext/bio/bigwig/libBigWig/test/testBigBed.c

@@ -1,132 +0,0 @@
-#include "bigWig.h"
-#include <stdio.h>
-#include <inttypes.h>
-#include <stdlib.h>
-#include <assert.h>
-
-void bwPrintHdr(bigWigFile_t *bb) {
-    uint64_t i;
-    int64_t i64;
-    printf("Version:    %"PRIu16"\n", bb->hdr->version);
-    printf("Levels:     %"PRIu16"\n", bb->hdr->nLevels);
-    printf("ctOffset:   0x%"PRIx64"\n", bb->hdr->ctOffset);
-    printf("dataOffset: 0x%"PRIx64"\n", bb->hdr->dataOffset);
-    printf("indexOffset:        0x%"PRIx64"\n", bb->hdr->indexOffset);
-    printf("fieldCount: %"PRIu32"\n", bb->hdr->fieldCount);
-    printf("definedFieldCount: %"PRIu32"\n", bb->hdr->definedFieldCount);
-    printf("sqlOffset:  0x%"PRIx64"\n", bb->hdr->sqlOffset);
-    printf("summaryOffset:      0x%"PRIx64"\n", bb->hdr->summaryOffset);
-    printf("bufSize:    %"PRIu32"\n", bb->hdr->bufSize);
-
-    if(bb->hdr->nLevels) {
-        printf("	i	level	data	index\n");
-    }
-    for(i=0; i<bb->hdr->nLevels; i++) {
-        printf("\t%"PRIu64"\t%"PRIu32"\t%"PRIx64"\t%"PRIx64"\n", i, bb->hdr->zoomHdrs->level[i], bb->hdr->zoomHdrs->dataOffset[i], bb->hdr->zoomHdrs->indexOffset[i]);
-    }
-
-    printf("nBasesCovered:      %"PRIu64"\n", bb->hdr->nBasesCovered);
-    printf("minVal:     %f\n", bb->hdr->minVal);
-    printf("maxVal:     %f\n", bb->hdr->maxVal);
-    printf("sumData:    %f\n", bb->hdr->sumData);
-    printf("sumSquared: %f\n", bb->hdr->sumSquared);
-
-    //Chromosome idx/name/length
-    if(bb->cl) {
-        printf("Chromosome List\n");
-        printf("  idx\tChrom\tLength (bases)\n");
-        for(i64=0; i64<bb->cl->nKeys; i64++) {
-            printf("  %"PRIu64"\t%s\t%"PRIu32"\n", i64, bb->cl->chrom[i64], bb->cl->len[i64]);
-        }
-    }
-}
-
-void bwPrintIndexNode(bwRTreeNode_t *node, int level) {
-    uint16_t i;
-    if(!node) return;
-    for(i=0; i<node->nChildren; i++) {
-        if(node->isLeaf) {
-            printf("  %i\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t0x%"PRIx64"\t%"PRIu64"\n", level,\
-                node->chrIdxStart[i], \
-                node->baseStart[i], \
-                node->chrIdxEnd[i], \
-                node->baseEnd[i], \
-                node->dataOffset[i], \
-                node->x.size[i]);
-        } else {
-            printf("  %i\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t0x%"PRIx64"\tNA\n", level,\
-                node->chrIdxStart[i], \
-                node->baseStart[i], \
-                node->chrIdxEnd[i], \
-                node->baseEnd[i], \
-                node->dataOffset[i]);
-            bwPrintIndexNode(node->x.child[i], level+1);
-        }
-    }
-}
-
-void bwPrintIndexTree(bigWigFile_t *fp) {
-    printf("\nIndex tree:\n");
-    printf("nItems:\t%"PRIu64"\n", fp->idx->nItems);
-    printf("chrIdxStart:\t%"PRIu32"\n", fp->idx->chrIdxStart);
-    printf("baseStart:\t%"PRIu32"\n", fp->idx->baseStart);
-    printf("chrIdxEnd:\t%"PRIu32"\n", fp->idx->chrIdxEnd);
-    printf("baseEnd:\t%"PRIu32"\n", fp->idx->baseEnd);
-    printf("idxSize:\t%"PRIu64"\n", fp->idx->idxSize);
-    printf("  level\tchrIdxStart\tbaseStart\tchrIdxEnd\tbaseEnd\tchild\tsize\n");
-    bwPrintIndexNode(fp->idx->root, 0);
-}
-
-int main(int argc, char *argv[]) {
-    bigWigFile_t *fp = NULL;
-    bbOverlappingEntries_t *o;
-    uint32_t i;
-    char *sql;
-    if(argc != 2) {
-        fprintf(stderr, "Usage: %s {file.bb|URL://path/file.bb}\n", argv[0]);
-        return 1;
-    }
-
-    if(bwInit(1<<17) != 0) {
-        fprintf(stderr, "Received an error in bwInit\n");
-        return 1;
-    }
-
-    assert(bwIsBigWig(argv[1], NULL) == 0);
-    assert(bbIsBigBed(argv[1], NULL) == 1);
-
-    fp = bbOpen(argv[1], NULL);
-    if(!fp) {
-        fprintf(stderr, "An error occured while opening %s\n", argv[1]);
-        return 1;
-    }
-
-    bwPrintHdr(fp);
-    bwPrintIndexTree(fp);
-
-    sql = bbGetSQL(fp);
-    if(sql) {
-        printf("SQL is: %s\n", sql);
-        free(sql);
-    }
-
-    //Presumably this is the sort of interface that's needed...
-    o = bbGetOverlappingEntries(fp, "chr1", 4450000, 4500000, 1);
-    printf("%"PRIu32" entries overlap\n", o->l);
-    for(i=0; i<o->l; i++) {
-        printf("%"PRIu32"-%"PRIu32"\t %s\n", o->start[i], o->end[i], o->str[i]);
-    }
-    if(o) bbDestroyOverlappingEntries(o);
-
-    //Ensure that we can fetch entries with no strings
-    o = bbGetOverlappingEntries(fp, "chr1", 4450000, 4500000, 0);
-    printf("%"PRIu32" entries overlap\n", o->l);
-    for(i=0; i<o->l; i++) {
-        printf("%"PRIu32"-%"PRIu32"\n", o->start[i], o->end[i]);
-    }
-    if(o) bbDestroyOverlappingEntries(o);
-
-    bwClose(fp);
-    bwCleanup();
-    return 0;
-}

data/ext/bio/bigwig/libBigWig/test/testIterator.c

@@ -1,67 +0,0 @@
-#include "bigWig.h"
-#include <stdio.h>
-#include <inttypes.h>
-#include <stdlib.h>
-#include <assert.h>
-
-int main(int argc, char *argv[]) {
-    bigWigFile_t *fp = NULL;
-    uint32_t i, chunk = 0, tid, blocksPerIteration;
-    char *sql, *chrom;
-    bwOverlapIterator_t *iter;
-    if(argc != 4) {
-        fprintf(stderr, "Usage: %s {file.bb|URL://path/file.bb} chromosome blocksPerIteration\n", argv[0]);
-        return 1;
-    }
-    chrom = argv[2];
-    blocksPerIteration = strtoul(argv[3], NULL, 10);
-
-    if(bwInit(1<<17) != 0) {
-        fprintf(stderr, "Received an error in bwInit\n");
-        return 1;
-    }
-
-    if(bwIsBigWig(argv[1], NULL)) {
-        fp = bwOpen(argv[1], NULL, "r");
-    } else if(bbIsBigBed(argv[1], NULL)) {
-        fp = bbOpen(argv[1], NULL);
-    }
-
-    if(!fp) {
-        fprintf(stderr, "An error occured while opening %s\n", argv[1]);
-        return 1;
-    }
-
-    sql = bbGetSQL(fp);
-    if(sql) {
-        printf("SQL is: %s\n", sql);
-        free(sql);
-    }
-
-    //So we can get the bounds
-    tid = bwGetTid(fp, chrom);
-
-    if(fp->type == 0) {
-        iter = bwOverlappingIntervalsIterator(fp, chrom, 0, fp->cl->len[tid], blocksPerIteration);
-    } else {
-        iter = bbOverlappingEntriesIterator(fp, chrom, 0, fp->cl->len[tid], 1, blocksPerIteration);
-    }
-    while(iter->data) {
-        if(fp->type == 0) {
-            for(i=0; i<iter->intervals->l; i++) {
-                printf("chunk %"PRIu32" entry %"PRIu32" %s:%"PRIu32"-%"PRIu32" %f\n", chunk, i, chrom, iter->intervals->start[i], iter->intervals->end[i], iter->intervals->value[i]);
-            }
-        } else {
-            for(i=0; i<iter->entries->l; i++) {
-                printf("chunk %"PRIu32" entry %"PRIu32" %s:%"PRIu32"-%"PRIu32" %s\n", chunk, i, chrom, iter->entries->start[i], iter->entries->end[i], iter->entries->str[i]);
-            }
-        }
-        chunk++;
-        iter = bwIteratorNext(iter);
-    }
-    bwIteratorDestroy(iter);
-
-    bwClose(fp);
-    bwCleanup();
-    return 0;
-}

data/ext/bio/bigwig/libBigWig/test/testLocal.c

@@ -1,223 +0,0 @@
-#include "bigWig.h"
-#include <stdio.h>
-#include <inttypes.h>
-#include <stdlib.h>
-#include <assert.h>
-
-void bwPrintHdr(bigWigFile_t *bw) {
-    uint64_t i;
-    int64_t i64;
-    printf("Version:    %"PRIu16"\n", bw->hdr->version);
-    printf("Levels:     %"PRIu16"\n", bw->hdr->nLevels);
-    printf("ctOffset:   0x%"PRIx64"\n", bw->hdr->ctOffset);
-    printf("dataOffset: 0x%"PRIx64"\n", bw->hdr->dataOffset);
-    printf("indexOffset:        0x%"PRIx64"\n", bw->hdr->indexOffset);
-    printf("sqlOffset:  0x%"PRIx64"\n", bw->hdr->sqlOffset);
-    printf("summaryOffset:      0x%"PRIx64"\n", bw->hdr->summaryOffset);
-    printf("bufSize:    %"PRIu32"\n", bw->hdr->bufSize);
-    printf("extensionOffset:    0x%"PRIx64"\n", bw->hdr->extensionOffset);
-
-    if(bw->hdr->nLevels) {
-        printf("	i	level	data	index\n");
-    }
-    for(i=0; i<bw->hdr->nLevels; i++) {
-        printf("\t%"PRIu64"\t%"PRIu32"\t%"PRIx64"\t%"PRIx64"\n", i, bw->hdr->zoomHdrs->level[i], bw->hdr->zoomHdrs->dataOffset[i], bw->hdr->zoomHdrs->indexOffset[i]);
-    }
-
-    printf("nBasesCovered:      %"PRIu64"\n", bw->hdr->nBasesCovered);
-    printf("minVal:     %f\n", bw->hdr->minVal);
-    printf("maxVal:     %f\n", bw->hdr->maxVal);
-    printf("sumData:    %f\n", bw->hdr->sumData);
-    printf("sumSquared: %f\n", bw->hdr->sumSquared);
-
-    //Chromosome idx/name/length
-    if(bw->cl) {
-        printf("Chromosome List\n");
-        printf("  idx\tChrom\tLength (bases)\n");
-        for(i64=0; i64<bw->cl->nKeys; i64++) {
-            printf("  %"PRIu64"\t%s\t%"PRIu32"\n", i64, bw->cl->chrom[i64], bw->cl->len[i64]);
-        }
-    }
-}
-
-void bwPrintIndexNode(bwRTreeNode_t *node, int level) {
-    uint16_t i;
-    if(!node) return;
-    for(i=0; i<node->nChildren; i++) {
-        if(node->isLeaf) {
-            printf("  %i\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t0x%"PRIx64"\t%"PRIu64"\n", level,\
-                node->chrIdxStart[i], \
-                node->baseStart[i], \
-                node->chrIdxEnd[i], \
-                node->baseEnd[i], \
-                node->dataOffset[i], \
-                node->x.size[i]);
-        } else {
-            printf("  %i\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t%"PRIu32"\t0x%"PRIx64"\tNA\n", level,\
-                node->chrIdxStart[i], \
-                node->baseStart[i], \
-                node->chrIdxEnd[i], \
-                node->baseEnd[i], \
-                node->dataOffset[i]);
-            bwPrintIndexNode(node->x.child[i], level+1);
-        }
-    }
-}
-
-void bwPrintIndexTree(bigWigFile_t *fp) {
-    printf("\nIndex tree:\n");
-    printf("nItems:\t%"PRIu64"\n", fp->idx->nItems);
-    printf("chrIdxStart:\t%"PRIu32"\n", fp->idx->chrIdxStart);
-    printf("baseStart:\t%"PRIu32"\n", fp->idx->baseStart);
-    printf("chrIdxEnd:\t%"PRIu32"\n", fp->idx->chrIdxEnd);
-    printf("baseEnd:\t%"PRIu32"\n", fp->idx->baseEnd);
-    printf("idxSize:\t%"PRIu64"\n", fp->idx->idxSize);
-    printf("  level\tchrIdxStart\tbaseStart\tchrIdxEnd\tbaseEnd\tchild\tsize\n");
-    bwPrintIndexNode(fp->idx->root, 0);
-}
-
-void printIntervals(bwOverlappingIntervals_t *ints, uint32_t start) {
-    uint32_t i;
-    if(!ints) return;
-    for(i=0; i<ints->l; i++) {
-        if(ints->start && ints->end) {
-            printf("Interval %"PRIu32"\t%"PRIu32"-%"PRIu32": %f\n",i, ints->start[i], ints->end[i], ints->value[i]);
-        } else if(ints->start) {
-            printf("Interval %"PRIu32"\t%"PRIu32"-%"PRIu32": %f\n",i, ints->start[i], ints->start[i]+1, ints->value[i]);
-        } else {
-            printf("Interval %"PRIu32"\t%"PRIu32"-%"PRIu32": %f\n",i, start+i, start+i+1, ints->value[i]);
-        }
-    }
-}
-
-int main(int argc, char *argv[]) {
-    bigWigFile_t *fp = NULL;
-    bwOverlappingIntervals_t *intervals = NULL;
-    double *stats = NULL;
-    if(argc != 2) {
-        fprintf(stderr, "Usage: %s {file.bw|URL://path/file.bw}\n", argv[0]);
-        return 1;
-    }
-
-    if(bwInit(1<<17) != 0) {
-        fprintf(stderr, "Received an error in bwInit\n");
-        return 1;
-    }
-
-    assert(bwIsBigWig(argv[1], NULL) == 1);
-    assert(bbIsBigBed(argv[1], NULL) == 0);
-
-    fp = bwOpen(argv[1], NULL, "r");
-    if(!fp) {
-        fprintf(stderr, "An error occured while opening %s\n", argv[1]);
-        return 1;
-    }
-
-    bwPrintHdr(fp);
-    bwPrintIndexTree(fp);
-
-    //Try to get some blocks
-    printf("1:0-99\n");
-    intervals = bwGetValues(fp, "1", 0, 99, 0);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("1:99-1000\n");
-    intervals = bwGetValues(fp, "1", 99, 1000, 0);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("1:99-150\n");
-    intervals = bwGetValues(fp, "1", 99, 150, 1);
-    printIntervals(intervals,99);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("1:99-100\n");
-    intervals = bwGetValues(fp, "1", 99, 100, 0);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("1:151-1000\n");
-    intervals = bwGetValues(fp, "1", 151, 1000, 0);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("chr1:0-100\n");
-    intervals = bwGetValues(fp, "chr1", 0, 100, 0);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    stats = bwStats(fp, "1", 0, 200, 1, mean);
-    assert(stats);
-    printf("1:0-1000 mean: %f\n", *stats);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 2, mean);
-    assert(stats);
-    printf("1:0-1000 mean: %f %f\n", stats[0], stats[1]);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 1, dev);
-    assert(stats);
-    printf("1:0-1000 std. dev.: %f\n", *stats);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 2, dev);
-    assert(stats);
-    printf("1:0-1000 std. dev.: %f %f\n", stats[0], stats[1]);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 1, min);
-    assert(stats);
-    printf("1:0-1000 min: %f\n", *stats);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 2, min);
-    assert(stats);
-    printf("1:0-1000 min: %f %f\n", stats[0], stats[1]);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 1, max);
-    assert(stats);
-    printf("1:0-1000 max: %f\n", *stats);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 2, max);
-    assert(stats);
-    printf("1:0-1000 max: %f %f\n", stats[0], stats[1]);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 1, cov);
-    assert(stats);
-    printf("1:0-1000 coverage: %f\n", *stats);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 2, cov);
-    assert(stats);
-    printf("1:0-1000 coverage: %f %f\n", stats[0], stats[1]);
-    free(stats);
-
-    stats = bwStats(fp, "1", 0, 200, 1, sum);
-    assert(stats);
-    printf("1:0-200 sum: %f\n", *stats); //72.1
-    free(stats);
-
-    stats = bwStats(fp, "1", 100, 151, 2, sum);
-    assert(stats);
-    printf("1:0-200 sum: %f %f\n", stats[0], stats[1]); //35.0, 36.5
-    free(stats);
-
-    printf("1:0-200000000 intervals\n");
-    intervals = bwGetOverlappingIntervals(fp, "1", 0, 200000000);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("10:0-200000000 intervals\n");
-    intervals = bwGetOverlappingIntervals(fp, "10", 0, 200000000);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    bwClose(fp);
-    bwCleanup();
-    return 0;
-}