bio-bigwig 0.0.1 → 0.0.2

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

@@ -1,296 +0,0 @@
-#ifndef NOCURL
-#include <curl/curl.h>
-#endif
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-#include "bigWigIO.h"
-#include <inttypes.h>
-#include <errno.h>
-
-size_t GLOBAL_DEFAULTBUFFERSIZE;
-
-#ifndef NOCURL
-uint64_t getContentLength(URL_t *URL) {
-    double size;
-    if(curl_easy_getinfo(URL->x.curl, CURLINFO_CONTENT_LENGTH_DOWNLOAD, &size) != CURLE_OK) {
-        return 0;
-    }
-    if(size== -1.0) return 0;
-    return (uint64_t) size;
-}
-
-//Fill the buffer, note that URL may be left in an unusable state on error!
-CURLcode urlFetchData(URL_t *URL, unsigned long bufSize) {
-    CURLcode rv;
-    char range[1024];
-
-    if(URL->filePos != (size_t) -1) URL->filePos += URL->bufLen;
-    else URL->filePos = 0;
-
-    URL->bufPos = URL->bufLen = 0; //Otherwise, we can't copy anything into the buffer!
-    sprintf(range,"%lu-%lu", URL->filePos, URL->filePos+bufSize-1);
-    rv = curl_easy_setopt(URL->x.curl, CURLOPT_RANGE, range);
-    if(rv != CURLE_OK) {
-        fprintf(stderr, "[urlFetchData] Couldn't set the range (%s)\n", range);
-        return rv;
-    }
-
-    rv = curl_easy_perform(URL->x.curl);
-    errno = 0; //Sometimes curl_easy_perform leaves a random errno remnant
-    return rv;
-}
-
-//Read data into a buffer, ideally from a buffer already in memory
-//The loop is likely no longer needed.
-size_t url_fread(void *obuf, size_t obufSize, URL_t *URL) {
-    size_t remaining = obufSize, fetchSize;
-    void *p = obuf;
-    CURLcode rv;
-
-    while(remaining) {
-        if(!URL->bufLen) {
-            rv = urlFetchData(URL, URL->bufSize);
-            if(rv != CURLE_OK) {
-                fprintf(stderr, "[url_fread] urlFetchData (A) returned %s\n", curl_easy_strerror(rv));
-                return 0;
-            }  
-        } else if(URL->bufLen < URL->bufPos + remaining) { //Copy the remaining buffer and reload the buffer as needed
-            p = memcpy(p, URL->memBuf+URL->bufPos, URL->bufLen - URL->bufPos);
-            if(!p) return 0;
-            p += URL->bufLen - URL->bufPos;
-            remaining -= URL->bufLen - URL->bufPos;
-            if(remaining) {
-                if(!URL->isCompressed) {
-                    fetchSize = URL->bufSize;
-                } else {
-                    fetchSize = (remaining<URL->bufSize)?remaining:URL->bufSize;
-                }
-                rv = urlFetchData(URL, fetchSize);
-                if(rv != CURLE_OK) {
-                    fprintf(stderr, "[url_fread] urlFetchData (B) returned %s\n", curl_easy_strerror(rv));
-                    return 0;
-                }
-            }
-        } else {
-            p = memcpy(p, URL->memBuf+URL->bufPos, remaining);
-            if(!p) return 0;
-            URL->bufPos += remaining;
-            remaining = 0;
-        }
-    }
-    return obufSize;
-}
-#endif
-
-//Returns the number of bytes requested or a smaller number on error
-//Note that in the case of remote files, the actual amount read may be less than the return value!
-size_t urlRead(URL_t *URL, void *buf, size_t bufSize) {
-#ifndef NOCURL
-    if(URL->type==0) {
-        return fread(buf, bufSize, 1, URL->x.fp)*bufSize;
-    } else {
-        return url_fread(buf, bufSize, URL);
-    }
-#else
-    return fread(buf, bufSize, 1, URL->x.fp)*bufSize;
-#endif
-}
-
-size_t bwFillBuffer(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;
-    if(!p) return 0;
-
-    p += URL->bufLen;
-    if(l*nmemb > URL->bufSize - URL->bufPos) { //We received more than we can store!
-        copied = URL->bufSize - URL->bufLen;
-    }
-    memcpy(p, inBuf, copied);
-    URL->bufLen += copied;
-
-    if(!URL->memBuf) return 0; //signal error
-    return copied;
-}
-
-//Seek to an arbitrary location, returning a CURLcode
-//Note that a local file returns CURLE_OK on success or CURLE_FAILED_INIT on any error;
-CURLcode urlSeek(URL_t *URL, size_t pos) {
-#ifndef NOCURL
-    char range[1024];
-    CURLcode rv;
-
-    if(URL->type == BWG_FILE) {
-#endif
-        if(fseek(URL->x.fp, pos, SEEK_SET) == 0) {
-            errno = 0;
-            return CURLE_OK;
-        } else {
-            return CURLE_FAILED_INIT; //This is arbitrary
-        }
-#ifndef NOCURL
-    } else {
-        //If the location is covered by the buffer then don't seek!
-        if(pos < URL->filePos || pos >= URL->filePos+URL->bufLen) {
-            URL->filePos = pos;
-            URL->bufLen = 0; //Otherwise, filePos will get incremented on the next read!
-            URL->bufPos = 0;
-            //Maybe this works for FTP?
-            sprintf(range,"%lu-%lu", pos, pos+URL->bufSize-1);
-            rv = curl_easy_setopt(URL->x.curl, CURLOPT_RANGE, range);
-            if(rv != CURLE_OK) {
-                fprintf(stderr, "[urlSeek] Couldn't set the range (%s)\n", range);
-                return rv;
-            }
-            rv = curl_easy_perform(URL->x.curl);
-            if(rv != CURLE_OK) {
-                fprintf(stderr, "[urlSeek] curl_easy_perform received an error!\n");
-            }
-            errno = 0;  //Don't propogate remnant resolved libCurl errors
-            return rv;
-        } else {
-            URL->bufPos = pos-URL->filePos;
-            return CURLE_OK;
-        }
-    }
-#endif
-}
-
-URL_t *urlOpen(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;
-#ifndef NOCURL
-    CURLcode code;
-    char range[1024];
-#endif
-
-    URL->fname = fname;
-
-    if((!mode) || (strchr(mode, 'w') == 0)) {
-        //Set the protocol
-#ifndef NOCURL
-        if(strncmp(fname, "http://", 7) == 0) URL->type = BWG_HTTP;
-        else if(strncmp(fname, "https://", 8) == 0) URL->type = BWG_HTTPS;
-        else if(strncmp(fname, "ftp://", 6) == 0) URL->type = BWG_FTP;
-        else URL->type = BWG_FILE;
-#else
-        URL->type = BWG_FILE;
-#endif
-
-        //local file?
-        if(URL->type == BWG_FILE) {
-            URL->filePos = -1; //This signals that nothing has been read
-            URL->x.fp = fopen(fname, "rb");
-            if(!(URL->x.fp)) {
-                free(URL);
-                fprintf(stderr, "[urlOpen] Couldn't open %s for reading\n", fname);
-                return NULL;
-            }
-#ifndef NOCURL
-        } else {
-            //Remote file, set up the memory buffer and get CURL ready
-            URL->memBuf = malloc(GLOBAL_DEFAULTBUFFERSIZE);
-            if(!(URL->memBuf)) {
-                free(URL);
-                fprintf(stderr, "[urlOpen] Couldn't allocate enough space for the file buffer!\n");
-                return NULL;
-            }
-            URL->bufSize = GLOBAL_DEFAULTBUFFERSIZE;
-            URL->x.curl = curl_easy_init();
-            if(!(URL->x.curl)) {
-                fprintf(stderr, "[urlOpen] curl_easy_init() failed!\n");
-                goto error;
-            }
-            //Negotiate a reasonable HTTP authentication method
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_HTTPAUTH, CURLAUTH_ANY) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Failed instructing curl to use any HTTP authentication it finds to be suitable!\n");
-                goto error;
-            }
-            //Follow redirects
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_FOLLOWLOCATION, 1L) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Failed instructing curl to follow redirects!\n");
-                goto error;
-            }
-            //Set the URL
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_URL, fname) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_URL!\n");
-                goto error;
-            }
-            //Set the range, which doesn't do anything for HTTP
-            sprintf(range, "0-%lu", URL->bufSize-1);
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_RANGE, range) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_RANGE (%s)!\n", range);
-                goto error;
-            }
-            //Set the callback info, which means we no longer need to directly deal with sockets and header!
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_WRITEFUNCTION, bwFillBuffer) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_WRITEFUNCTION!\n");
-                goto error;
-            }
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_WRITEDATA, (void*)URL) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_WRITEDATA!\n");
-                goto error;
-            }
-            //Ignore certificate errors with https, libcurl just isn't reliable enough with conda
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_SSL_VERIFYPEER, 0) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_SSL_VERIFYPEER to 0!\n");
-                goto error;
-            }
-            if(curl_easy_setopt(URL->x.curl, CURLOPT_SSL_VERIFYHOST, 0) != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_SSL_VERIFYHOST to 0!\n");
-                goto error;
-            }
-            if(callBack) {
-                code = callBack(URL->x.curl);
-                if(code != CURLE_OK) {
-                    fprintf(stderr, "[urlOpen] The user-supplied call back function returned an error: %s\n", curl_easy_strerror(code));
-                    goto error;
-                }
-            }
-            code = curl_easy_perform(URL->x.curl);
-            errno = 0; //Sometimes curl_easy_perform leaves a random errno remnant
-            if(code != CURLE_OK) {
-                fprintf(stderr, "[urlOpen] curl_easy_perform received an error: %s\n", curl_easy_strerror(code));
-                goto error;
-            }
-#endif
-        }
-    } else {
-        URL->type = BWG_FILE;
-        URL->x.fp = fopen(fname, mode);
-        if(!(URL->x.fp)) {
-            free(URL);
-            fprintf(stderr, "[urlOpen] Couldn't open %s for writing\n", fname);
-            return NULL;
-        }
-    }
-    if(url) free(url);
-    if(req) free(req);
-    return URL;
-
-#ifndef NOCURL
-error:
-    if(url) free(url);
-    if(req) free(req);
-    free(URL->memBuf);
-    curl_easy_cleanup(URL->x.curl);
-    free(URL);
-    return NULL;
-#endif
-}
-
-//Performs the necessary free() operations and handles cleaning up curl
-void urlClose(URL_t *URL) {
-    if(URL->type == BWG_FILE) {
-        fclose(URL->x.fp);
-#ifndef NOCURL
-    } else {
-        free(URL->memBuf);
-        curl_easy_cleanup(URL->x.curl);
-#endif
-    }
-    free(URL);
-}

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;
-}