bio-bigwig 0.0.1 → 0.0.2

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;
-}

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

@@ -1,203 +0,0 @@
-#include "bigWig.h"
-#include <stdio.h>
-#include <inttypes.h>
-#include <stdlib.h>
-#include <assert.h>
-
-//Print overly verbose header information
-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]);
-        }
-    }
-}
-
-//This is an example call back function
-CURLcode callBack(CURL *curl) {
-    CURLcode rv;
-
-    rv = curl_easy_setopt(curl, CURLOPT_USERNAME, "anonymous");
-    if(rv != CURLE_OK) return rv;
-
-    rv = curl_easy_setopt(curl, CURLOPT_PASSWORD, "libBigWig@github.com");
-    return rv;
-}
-
-int main(int argc, char *argv[]) {
-    bigWigFile_t *fp = NULL;
-    bwOverlappingIntervals_t *intervals = NULL;
-    double *stats = NULL;
-    char chrom[] = "chr1";
-    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;
-    }
-
-    fp = bwOpen(argv[1], callBack, "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("%s:10000000-10000100 Intervals\n", chrom);
-    intervals = bwGetOverlappingIntervals(fp, chrom, 10000000, 10000100);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    printf("%s:10000000-10000100 Values\n", chrom);
-    intervals = bwGetValues(fp, chrom, 10000000, 10000100, 0);
-    printIntervals(intervals,0);
-    bwDestroyOverlappingIntervals(intervals);
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 1, mean);
-    if(stats) {
-        printf("%s:10000000-10000100 mean: %f\n", chrom, stats[0]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 2, mean);
-    if(stats) {
-        printf("%s:10000000-10000100 mean: %f %f\n", chrom, stats[0], stats[1]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 1, dev);
-    if(stats) {
-        printf("%s:10000000-10000100 std. dev.: %f\n", chrom, stats[0]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 2, dev);
-    if(stats) {
-        printf("%s:10000000-10000100 std. dev.: %f %f\n", chrom, stats[0], stats[1]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 1, min);
-    if(stats) {
-        printf("%s:10000000-10000100 min: %f\n", chrom, stats[0]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 2, min);
-    if(stats) {
-        printf("%s:10000000-10000100 min: %f %f\n", chrom, stats[0], stats[1]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 1, max);
-    if(stats) {
-        printf("%s:10000000-10000100 max: %f\n", chrom, stats[0]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 2, max);
-    if(stats) {
-        printf("%s:10000000-10000100 max: %f %f\n", chrom, stats[0], stats[1]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 1, cov);
-    if(stats) {
-        printf("%s:10000000-10000100 coverage: %f\n", chrom, stats[0]);
-        free(stats);
-    }
-
-    stats = bwStats(fp, chrom, 10000000, 10000100, 2, cov);
-    if(stats) {
-        printf("%s:10000000-10000100 coverage: %f %f\n", chrom, stats[0], stats[1]);
-        free(stats);
-    }
-
-    bwClose(fp);
-    bwCleanup();
-    return 0;
-}

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

@@ -1,46 +0,0 @@
-#include "bigWig.h"
-#include <stdio.h>
-#include <inttypes.h>
-#include <stdlib.h>
-#include <assert.h>
-
-//This is an example call back function
-CURLcode callBack(CURL *curl) {
-    CURLcode rv;
-
-    rv = curl_easy_setopt(curl, CURLOPT_USERNAME, "anonymous");
-    if(rv != CURLE_OK) return rv;
-
-    rv = curl_easy_setopt(curl, CURLOPT_PASSWORD, "libBigWig@github.com");
-    return rv;
-}
-
-int main(int argc, char *argv[]) {
-    bigWigFile_t *fp = NULL;
-    int64_t i;
-
-    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;
-    }
-
-    fp = bwOpen(argv[1], callBack, "r");
-    if(!fp) {
-        fprintf(stderr, "An error occured while opening %s\n", argv[1]);
-        return 1;
-    }
-
-    //Return the number of chromosomes/contigs
-    for(i=0; i<fp->cl->nKeys; i++) {
-        printf("%s\t%"PRIu32"\n", fp->cl->chrom[i], fp->cl->len[i]);
-    }
-
-    bwClose(fp);
-    bwCleanup();
-    return 0;
-}

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

@@ -1,68 +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 *ifp = NULL;
-    bigWigFile_t *ofp = NULL;
-    uint32_t tid, i;
-    char **chroms;
-    bwOverlappingIntervals_t *o;
-    if(argc != 3) {
-        fprintf(stderr, "Usage: %s {inputfile.bw|URL://path/inputfile.bw} outputfile.bw\n", argv[0]);
-        return 1;
-    }
-
-    if(bwInit(1<<17) != 0) {
-        fprintf(stderr, "Received an error in bwInit\n");
-        return 1;
-    }
-
-    ifp = bwOpen(argv[1], NULL, "r");
-    if(!ifp) {
-        fprintf(stderr, "An error occured while opening %s\n", argv[1]);
-        return 1;
-    }
-
-    ofp = bwOpen(argv[2], NULL, "w");
-    if(!ofp) {
-        bwClose(ifp);
-        fprintf(stderr, "An error occured while opening %s\n", argv[2]);
-        return 1;
-    }
-
-    if(bwCreateHdr(ofp, 10)) goto error; //ten zoom levels
-    ofp->cl = bwCreateChromList(ifp->cl->chrom, ifp->cl->len, ifp->cl->nKeys);
-    if(!ofp->cl) goto error;
-
-    if(bwWriteHdr(ofp)) goto error;
-
-    //Copy all of the intervals
-    for(tid = 0; tid < ofp->cl->nKeys; tid++) {
-        o = bwGetOverlappingIntervals(ifp, ofp->cl->chrom[tid], 0, ofp->cl->len[tid]);
-        if(!o) goto error;
-        if(o->l) {
-            chroms = malloc(o->l * sizeof(char*));
-            if(!chroms) goto error;
-            for(i=0; i<o->l; i++) chroms[i] = ofp->cl->chrom[tid];
-            bwAddIntervals(ofp, chroms, o->start, o->end, o->value, o->l);
-            free(chroms);
-        }
-        bwDestroyOverlappingIntervals(o);
-    }
-
-    bwClose(ifp);
-    bwClose(ofp);
-    bwCleanup();
-
-    return 0;
-
-error:
-    fprintf(stderr, "Got an error somewhere!\n");
-    bwClose(ifp);
-    bwClose(ofp);
-    bwCleanup();
-    return 1;
-}