bio-twobit 0.2.2 → 0.2.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -2,7 +2,8 @@
 
 [![Gem Version](https://badge.fury.io/rb/bio-twobit.svg)](https://badge.fury.io/rb/bio-twobit)
 [![test](https://github.com/kojix2/bio-twobit/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/bio-twobit/actions/workflows/ci.yml)
-[![dics](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/bio-twobit)
+[![docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/bio-twobit)
+[![Lines of Code](https://img.shields.io/endpoint?url=https%3A%2F%2Ftokei.kojix2.net%2Fbadge%2Fgithub%2Fkojix2%2Fbio-twobit%2Flines)](https://tokei.kojix2.net/github/kojix2/bio-twobit)
 [![DOI](https://zenodo.org/badge/436454379.svg)](https://zenodo.org/badge/latestdoi/436454379)
 
 Bio::TwoBit is a Ruby interface to 2bit files.

data/ext/bio/twobit/2bit.c

@@ -18,7 +18,8 @@ uint64_t twobitTell(TwoBit *tb);
 */
 size_t twobitRead(void *data, size_t sz, size_t nmemb, TwoBit *tb) {
     if(tb->data) {
-        if(memcpy(data, tb->data + tb->offset, nmemb * sz) == NULL) return 0;
+        // tb->data is a void*, so perform byte-wise pointer arithmetic via a char* cast
+        if(memcpy(data, (const char*)tb->data + tb->offset, nmemb * sz) == NULL) return 0;
         tb->offset += nmemb * sz;
         return nmemb;
     } else {
@@ -69,7 +70,7 @@ void bytes2bases(char *seq, uint8_t *byte, uint32_t sz, int offset) {
 
     // Deal with the first partial byte
     if(offset != 0) {
-        while(offset < 4) {
+        while(offset < 4 && pos < sz) {
            seq[pos++] = byte2base(foo, offset++);
         }
         if(pos >= sz) return;
@@ -204,15 +205,17 @@ error:
 */
 char *twobitSequence(TwoBit *tb, char *chrom, uint32_t start, uint32_t end) {
     uint32_t i, tid=0;
+    int found = 0;
 
     //Get the chromosome ID
     for(i=0; i<tb->hdr->nChroms; i++) {
         if(strcmp(tb->cl->chrom[i], chrom) == 0) {
             tid = i;
+            found = 1;
             break;
         }
     }
-    if(tid == 0 && strcmp(tb->cl->chrom[i], chrom) != 0) return NULL;
+    if(!found) return NULL;
 
     //Get the start/end if not specified
     if(start == end && end == 0) {
@@ -309,13 +312,13 @@ void *twobitBasesWorker(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end,
 
     while(i < len) {
         // Check if we need to jump
-        if(maskIdx != -1 && start + i + 4 >= maskStart) {
+        if(maskIdx != (uint32_t)-1 && start + i + 4 >= maskStart) {
             if(start + i >= maskStart || start + i + 4 - offset > maskStart) {
                 //Jump iff the whole byte is inside an N block
                 if(start + i >= maskStart && start + i + 4 - offset < maskEnd) {
                     //iff we're fully in an N block then jump
                     i = maskEnd - start;
-                    getMask(tb, tid, i, end, &maskIdx, &maskStart, &maskEnd);
+                    getMask(tb, tid, start + i, end, &maskIdx, &maskStart, &maskEnd);
                     offset = (start + i) % 4;
                     j = i / 4;
                     mask = getByteMaskFromOffset(offset);
@@ -331,7 +334,7 @@ void *twobitBasesWorker(TwoBit *tb, uint32_t tid, uint32_t start, uint32_t end,
                 if(mask & 4 && (foo + 1 >= maskStart && foo + 1 < maskEnd)) mask -= 4;
                 if(mask & 8 && (foo >= maskStart && foo < maskEnd)) mask -= 8;
                 if(foo + 4 > maskEnd) {
-                    getMask(tb, tid, i, end, &maskIdx, &maskStart, &maskEnd);
+                    getMask(tb, tid, start + i, end, &maskIdx, &maskStart, &maskEnd);
                     continue;
                 }
             }
@@ -397,16 +400,18 @@ error:
 
 void *twobitBases(TwoBit *tb, char *chrom, uint32_t start, uint32_t end, int fraction) {
     uint32_t tid = 0, i;
+    int found = 0;
 
     //Get the chromosome ID
     for(i=0; i<tb->hdr->nChroms; i++) {
         if(strcmp(tb->cl->chrom[i], chrom) == 0) {
             tid = i;
+            found = 1;
             break;
         }
     }
 
-    if(tid == 0 && strcmp(tb->cl->chrom[i], chrom) != 0) return NULL;
+    if(!found) return NULL;
 
     //Get the start/end if not specified
     if(start == end && end == 0) {
@@ -510,13 +515,13 @@ error:
             for(i=0; i<tb->hdr->nChroms; i++) {
                 if(idx->nBlockStart[i]) free(idx->nBlockStart[i]);
             }
-            free(idx->nBlockStart[i]);
+            free(idx->nBlockStart);
         }
         if(idx->nBlockSizes) {
             for(i=0; i<tb->hdr->nChroms; i++) {
                 if(idx->nBlockSizes[i]) free(idx->nBlockSizes[i]);
             }
-            free(idx->nBlockSizes[i]);
+            free(idx->nBlockSizes);
         }
 
         if(idx->maskBlockCount) free(idx->maskBlockCount);
@@ -524,13 +529,13 @@ error:
             for(i=0; i<tb->hdr->nChroms; i++) {
                 if(idx->maskBlockStart[i]) free(idx->maskBlockStart[i]);
             }
-            free(idx->maskBlockStart[i]);
+            free(idx->maskBlockStart);
         }
         if(idx->maskBlockSizes) {
             for(i=0; i<tb->hdr->nChroms; i++) {
                 if(idx->maskBlockSizes[i]) free(idx->maskBlockSizes[i]);
             }
-            free(idx->maskBlockSizes[i]);
+            free(idx->maskBlockSizes);
         }
 
         if(idx->offset) free(idx->offset);
@@ -706,12 +711,13 @@ TwoBit* twobitOpen(char *fname, int storeMasked) {
     fd = fileno(tb->fp);
     if(fstat(fd, &fs) == 0) {
         tb->sz = (uint64_t) fs.st_size;
-        tb->data = mmap(NULL, fs.st_size, PROT_READ, MAP_SHARED, fd, 0);
-        if(tb->data) {
-            if(madvise(tb->data, fs.st_size, MADV_RANDOM) != 0) {
-                munmap(tb->data, fs.st_size);
-                tb->data = NULL;
-            }
+        void *map = mmap(NULL, fs.st_size, PROT_READ, MAP_SHARED, fd, 0);
+        if(map != MAP_FAILED) {
+            tb->data = map;
+            /* madvise is an optional optimization; ignore failures */
+            madvise(tb->data, fs.st_size, MADV_RANDOM);
+        } else {
+            tb->data = NULL; /* mmap failed */
         }
     }
 

data/lib/bio/twobit/version.rb

@@ -2,6 +2,6 @@
 
 module Bio
   class TwoBit
-    VERSION = "0.2.2"
+    VERSION = "0.2.4"
   end
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: bio-twobit
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.4
 platform: ruby
 authors:
 - kojix2
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-09-19 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies: []
 description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
   which provides high-speed access to genomic data in 2bit file format.
@@ -146,7 +145,6 @@ homepage: https://github.com/kojix2/bio-twobit
 licenses:
 - MIT
 metadata: {}
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -161,8 +159,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.16
-signing_key:
+rubygems_version: 3.6.9
 specification_version: 4
 summary: A ruby library for accessing 2bit files
 test_files: []