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Bam reader robustness; allow threaded bam reading from Python
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@ -4465,6 +4465,9 @@ complete_pointers(TypedWritable **p_list, BamReader *manager) {
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set_fancy_bit(FB_effects, !_effects->is_empty());
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set_fancy_bit(FB_effects, !_effects->is_empty());
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set_fancy_bit(FB_tag, !_tag_data.empty());
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set_fancy_bit(FB_tag, !_tag_data.empty());
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// Mark the bounds stale.
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++_next_update;
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return pi;
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return pi;
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}
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}
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@ -142,6 +142,12 @@ init() {
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_file_stdfloat_double = scan.get_bool();
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_file_stdfloat_double = scan.get_bool();
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}
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}
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if (scan.get_current_index() > header.get_length()) {
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bam_cat.error()
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<< "Bam header is too short.\n";
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return false;
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}
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return true;
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return true;
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}
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}
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@ -1230,6 +1236,12 @@ p_read_object() {
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int object_id = read_object_id(scan);
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int object_id = read_object_id(scan);
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if (scan.get_current_index() > dg.get_length()) {
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bam_cat.error()
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<< "Found truncated datagram in bam stream\n";
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return 0;
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}
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// There are two cases (not counting the special _remove_flag case,
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// There are two cases (not counting the special _remove_flag case,
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// above). Either this is a new object definition, or this is a
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// above). Either this is a new object definition, or this is a
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// reference to an object that was previously defined.
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// reference to an object that was previously defined.
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@ -1271,6 +1283,12 @@ p_read_object() {
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created_obj._ptr->fillin(scan, this);
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created_obj._ptr->fillin(scan, this);
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_now_creating = was_creating;
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_now_creating = was_creating;
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if (scan.get_remaining_size() > 0) {
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bam_cat.warning()
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<< "Skipping " << scan.get_remaining_size() << " remaining bytes "
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<< "in datagram containing type " << type << "\n";
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}
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} else {
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} else {
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// We are receiving a new object. Now we can call the factory
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// We are receiving a new object. Now we can call the factory
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// to create the object.
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// to create the object.
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@ -1371,6 +1389,13 @@ p_read_object() {
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}
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}
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}
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}
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}
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}
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// Sanity check that we read the expected number of bytes.
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if (scan.get_current_index() > dg.get_length()) {
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bam_cat.error()
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<< "End of datagram reached while reading bam object "
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<< type << ": " << (void *)created_obj._ptr << "\n";
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}
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}
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}
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return object_id;
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return object_id;
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@ -144,8 +144,8 @@ PUBLISHED:
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INLINE const LoaderOptions &get_loader_options() const;
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INLINE const LoaderOptions &get_loader_options() const;
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INLINE void set_loader_options(const LoaderOptions &options);
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INLINE void set_loader_options(const LoaderOptions &options);
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TypedWritable *read_object();
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BLOCKING TypedWritable *read_object();
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bool read_object(TypedWritable *&ptr, ReferenceCount *&ref_ptr);
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BLOCKING bool read_object(TypedWritable *&ptr, ReferenceCount *&ref_ptr);
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INLINE bool is_eof() const;
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INLINE bool is_eof() const;
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bool resolve();
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bool resolve();
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