gentoo resync : 10.12.2017

5 files changed, 10 insertions, 720 deletions

diff --git a/sci-biology/goby-cpp/Manifest b/sci-biology/goby-cpp/Manifest
index a0cf57197f35..c38de79d4ffa 100644
--- a/sci-biology/goby-cpp/Manifest
+++ b/sci-biology/goby-cpp/Manifest
@@ -1,10 +1,8 @@
-AUX Alignments.proto 26192 BLAKE2B 412eb735feb2e1a9b85f4b9ee24620052648f292f041968a2d7bfae52c124697a40813467c038da44b18a89c2e9dc554bf93c414553bd1397829205af2f0f632 SHA512 c5b67577bfd8432e64489dfb08333adcece8712a398497facb284b52c5b773eff79d71c6dc5bcb72ab21b977423530e27cac3fa2a888c3a00cca1a09faf1b00f
-AUX Reads.proto 3128 BLAKE2B 38af9aa9ac3e792791ee90a2506419dd2356618200c16924929796160c98b4cb5b2ca8ecb2b66085605b86227dc04f155f1c6610c07577ec0fbb3bde69da2384 SHA512 eed972f7f054096ba0e4b215e1551b8acdee6024cec6091abe2b92e268b09fb77d2e9c2a90520611da3bfe37e69a8341e406c4eccb57b0c88f3664f7f2818e27
-AUX goby-cpp-2.0.1-underlinking.patch 708 BLAKE2B c0b5e6607708dfb0329e0f81292197241c7b79a3521fbea1607225d1350e7cbdbcbecb5755fab545421801b73eba0e89eaa7a246a2e6d3b91d811f6bacfe456b SHA512 511b91d704c981bf54d62b181c7244a1506b792897773ded7b836cbda32dfe3c4f9ab96260d6700fe665adbc7dd84a67dcbfbbb1f817c7f27aab46f8ac6bf8f0
-DIST goby_1.9.7.3-cpp.zip 127215 SHA256 8493daa7c850732c6c48d4512bd26b7eec411a729b39d9861a4a6aae08faa674 SHA512 56bf190224b6f22e0578cea4cc950e52e746655c75ffc13675276787b4d0ced682f891f6ecf7af3cf124b535ac3afc8711b0ecff44d6fd25fe521de7371c3486 WHIRLPOOL ae7ead1b0364383b46d4ef8b59453146c68384b379c26498fc9b24d014ba096a99723bad42cfeb84d44c20e4fc14882bbad303ab8c981889f90dff88a882c5c0
-DIST goby_1.9.8.1-cpp.zip 134904 SHA256 2f1bd87f2870af178f34a8e7c11819aa9e42f35e20f1985d2ceb054f452e2a97 SHA512 d31cd7f0be19074bfe8da74d9f2510f0e0f15fe6c485bbed8520052468d2cd2f1bc5fcad8b0d6a1586f5acde73db326059f45994ecfbb5fb6c09692d8e155190 WHIRLPOOL 6ce51c46f8802d31068f510f6da13b2920086eafdae24506830b42d79e48eb6ed9cac48a96090a81964daebf4a0c8f21c490ca3b0af2f589ac57647bde1be79f
-DIST goby_2.0.1-cpp.zip 177718 SHA256 5ec57b833cb1a0f53e975112d1c360b14a9b17cfff3fb0ad77dd70672c1881db SHA512 992bd10d5538dec1478820f26151dd311f4de13e7947b49f0b06d6cbdd4b71deeb3aa8a4c6a598fb92fbcb9cbf4ff97bf81205c9389d4a0da4443317e48aea9f WHIRLPOOL ab94cf674703917b6f0cde812d0fbcd94e18fb6055b30d6a1eefa1e4cb5b76bbe18c67388c66e25e87e522df9a9946b0eae5a164428abe874a382f5bc39a13d0
+DIST goby-cpp-2.0.1-files.tar.bz2 8354 BLAKE2B 0169e1bbcdc27f359cde47df708546dd6af0a68334295b247a6aac9122b7e9b1ee590fe0b57052c642b7e25478f5b118c70bec0c4b4af3694ab0f68c1c9ea73a SHA512 6f0cf466688cdbe9fe646cdff78dd0721fd0b0819c354c63e7c39c45895c319754cdadf23aeb9d544b0b2c68f1168583cb541ec160ba7f567fa0218dbad38e1e
+DIST goby_1.9.7.3-cpp.zip 127215 BLAKE2B 0673c36b503a6daee5fdaaf96fb415277502c0a49e530eb39983d4718f4a1d8eb9a6ff0a3202413c358600aafc2bf73482be12462f798923c13e19a6bcd590b1 SHA512 56bf190224b6f22e0578cea4cc950e52e746655c75ffc13675276787b4d0ced682f891f6ecf7af3cf124b535ac3afc8711b0ecff44d6fd25fe521de7371c3486
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+DIST goby_2.0.1-cpp.zip 177718 BLAKE2B 666b50fdc199693f8a4f9b6007f6609e91ab6093b643da88e580c9a3438a150cd7be78d2b5dcdd2fe905263d32ebbac1e0e47dbc637fd5d59f877e7cbdaaeeb2 SHA512 992bd10d5538dec1478820f26151dd311f4de13e7947b49f0b06d6cbdd4b71deeb3aa8a4c6a598fb92fbcb9cbf4ff97bf81205c9389d4a0da4443317e48aea9f
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diff --git a/sci-biology/goby-cpp/files/Alignments.proto b/sci-biology/goby-cpp/files/Alignments.proto
deleted file mode 100644
index fe7f56647644..000000000000
--- a/sci-biology/goby-cpp/files/Alignments.proto
+++ /dev/null
@@ -1,597 +0,0 @@
-package goby;
-
-option java_package = "edu.cornell.med.icb.goby.alignments";
-
-option optimize_for = SPEED;
-
-/*
-  This message is written to 'basename'.entries as a very large chunked collection.
-*/
-message AlignmentCollection {
-    repeated AlignmentEntry alignment_entries = 1;
-}
-
-
-message AlignmentEntry {
-    /* Multiplicity of this entry. The number of times this  alignment entry would be repeated exactly the same if
-     query redundancy had not been removed by read factorization.
-    */
-    optional uint32 multiplicity = 7;
-
-    /*
-      Compressed stream of data. Removed since Goby 2.0 supports chunk codecs. Do not reuse field index 23
-      optional bytes compressed_data = 23;
-    */
-
-    /* An integer that uniquely identifies the query (a short read) in a set of alignment runs. When several
-      alignment runs are made with the same set of query sequences, equality of query index means that the query
-      sequences were the same. (Comparing integers for equality is much faster than comparing strings.)
-      This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 query_index = 1;
-    /* An integer that uniquely identifies the target (e.g., a chromosome) in a set of alignment runs. When several
-      alignment runs are made with the same set of target sequences, equality of target index means that the target
-      sequence was the same across the runs. (Comparing integers for equality is much faster than comparing strings.)
-      This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 target_index = 2;
-    /*
-     The position on the target of the start of the alignment between the query and the target.
-     In the following example, position is 3 because the third base of the query 'C' was aligned with
-     position 3 of the reference (two read bases were soft clipped: "ct"). This example shows that the
-     alignment can start at a mismatch if it was so constructed by the aligner.
-
-     0123456789
-     AAAAGTCAAA  target
-      ctCGTC     query
-    This field is required (enforced by semantic validation in Goby 2.0+).
-   */
-    optional uint32 position = 3;
-
-    /*
-       True when the query matches the target on the reverse strand
-    */
-    optional bool matching_reverse_strand = 6;
-
-    /*
-     The position on the query where the alignment starts. This value is different from zero
-     when some bases/residues of the query could not be aligned with the target.
-     TODO: Rename this to left_trim. Add a right_trim property.
-    */
-    optional uint32 query_position = 5;
-
-    /*
-     The score of the alignment, where larger scores indicate better matches between the query and the target.
-     If an aligner outputs only the number of mismatches between query and target, the score is taken to be
-     -(#mismatches(query,target)).
-    */
-    optional float score = 4;
-
-    /*
-      Number of bases/residues that differ in the alignment between query and target sequences.
-    */
-    optional uint32 number_of_mismatches = 8;
-
-    /*
-     Cumulative number of insertions and/or deletions present in the alignment.
-    */
-    optional uint32 number_of_indels = 9;
-
-    /*
-     Number of bases that have been aligned for the query. Please note that query_aligned_length must be
-     less or equal to query_length.
-    */
-    optional uint32 query_aligned_length = 11;
-
-    /*
-     Number of bases that have been aligned for the target.
-    */
-    optional uint32 target_aligned_length = 12;
-
-    repeated SequenceVariation sequence_variations = 13;
-
-    /*
-     Length of the query sequence.
-    */
-    optional uint32 query_length = 10;
-    /*
-      Mapping Quality (phred-scaled posterior probability that the mapping
-      position of this read is incorrect). Please note that different aligners
-      may estimate mapping quality with different approaches, resulting in aligner
-      specific differences in the distribution of mapping quality. It is recommended
-      to condition mapping quality on the aligner that produced the specific alignment
-      being processed. See aligner name and version in the header.
-      Note that the following description is preliminary. A clear specification is
-      needed:
-      The mapping quality should be proportional to the
-      log of the probability that the given mapping is the "correct" one.
-      So if there are five equally good mappings of a read to the genome,
-      the probability of each would be 0.2, and the mapping quality would be
-      something like -10*log10(1-0.2) = 1.  If a mapping is highly likely,
-      say a 1e-4 of it being wrong, then the mapping quality would be
-      -10*log10(1e-4) = 40.
-    */
-    optional int32 mapping_quality = 14;
-
-    /*
-       If this read was aligned with a pair, the flags for the pair alignment (based on SAM):
-          000000001    paired
-          000000010    properly paired
-          000000100    read unmapped
-          000001000    mate unmapped
-          000010000    read reverse strand
-          000100000    mate reverse strand
-          001000000    first in pair
-          010000000    second in pair
-          100000000    not primary alignment
-    */
-    optional uint32 pair_flags = 15;
-
-    /*
-     If there is an alignment entry for the paired read (the paired read was mapped), a link to the entry is given.
-    */
-    optional RelatedAlignmentEntry pair_alignment_link = 16;
-
-    /* Index of the read fragment from which this alignment was obtained. */
-    optional uint32 fragment_index = 17;
-
-    /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more
-      alignment entries, one for each matching part of the read, and link these entries with
-      spliced_alignment_links. The field spliced_forward_alignment_link points to the next
-      AlignmentEntry in the chain of spliced alignments.
-    */
-    optional RelatedAlignmentEntry spliced_forward_alignment_link = 18;
-
-    /* If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two or more
-      alignment entries, one for each matching part of the read, and link these entries with
-      spliced_alignment_links. The field spliced_backward_alignment_link points to the previous
-      AlignmentEntry in the chain of spliced alignments.
-    */
-    optional RelatedAlignmentEntry spliced_backward_alignment_link = 22;
-
-    /*
-      If a read spans exon-exon junctions some aligners (e.g., GSNAP) will output two alignment entries, one for each
-      matching part of the read, and flag describes the spliced_alignment_link with these
-      binary flags:
-        000000001    normal
-        000000010    novel
-    */
-    optional uint32 spliced_flags = 19;
-
-    /* The size of the insert used when making the sequence library. This is the total size of the DNA
-    fragment to sequence, without the adapters. This is not the length of sequence that separates the reads.
-    See http://seqanswers.com/forums/showthread.php?t=8730 for details. Insert size is inferred for each pair
-    of reads by the aligner and is recorded here if was estimated (i.e., for paired-end reads).
-    */
-    optional sint32 insert_size = 20;
-
-    /*
-       The sample index. Uniquely identifies the aligned sample this read was read from. Storing the sample index in the
-       alignment entry makes it possible to concat alignments from different origins and track what sample originally
-       contained each entry.
-    */
-    optional uint32 sample_index = 21;
-    /*
-        The total number of times the query index associated with this entry occurs across the entire alignment file.
-
-        This field is used to purge queryIndex->smallIndex associations after all instances of a queryindex have
-        been seen (see QueryIndexPermutation class). When each entry has a value for this field, the header field
-        query_index_occurrences is true.
-        This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 query_index_occurrences = 25;
-    /*
-        The total number of times the read matches the reference across the entire alignment file. This differs from
-        query_index_occurrences because reads that are matching through splice and pair links count as one for ambiguity.
-        The field can be used to filter by ambiguity-threshold on the fly after an alignment has been done (to restrict
-        entries to more smaller thresholds). When each entry has a value for this field, the header field
-        ambiguity_stored_in_entries is true.
-
-        This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 ambiguity = 27;
-    /*
-        List of BAM attributes, if the alignment was imported from BAM. The attributes are stored in exactly the format
-        allowed for BAM. For instance, X0:i:9  X1:i:1  MD:Z:68 RG:Z:SRR084825 will be stored as four strings:
-        "X0:i:9", "X1:i:1", "MD:Z:68", "RG:Z:SRR084825". Note that sam-to-compact will interpret some BAM attributes
-        and populate goby native fields. Such tags do not appear in bam_attributes, and are instead re-generated from
-        the corresponding goby native fields.
-        Since Goby 2.0.
-    */
-    repeated string bam_attributes = 50;
-    /*
-        Quality scores for all bases of the read.
-        Since Goby 2.0.
-    */
-    optional bytes read_quality_scores = 55;
-
-    /*
-        Origin index. An integer that references a ReadOriginInfo message in the alignment header and
-        makes it possible to track the origin of the read (especially useful after several alignments
-        have been merged/concatenated).
-        (Since Goby 2.0).
-    */
-    optional uint32 read_origin_index = 26;
-    /*
-    Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially
-    erroneous bases, or bases that belong to a different part of the reference genome. Left clipped bases are
-    stored in this field as character bases, or as an equal sign character '=' when the clipped base did match
-    the reference base. For instance "A=G" for three soft-clipped bases, the middle one matching the genome at
-    this position. The number of bases in softClippedBasesLeft is exactly equal to queryPosition.
-    */
-    optional string softClippedBasesLeft = 30;
-    /*
-    Bases that an aligner considered do not belong to the alignment of the read to the reference. Potentially
-    erroneous bases, or bases that belong to a different part of the reference genome. Right clipped bases are
-    stored in this field as character bases, or as an equal sign character '=' when the clipped base did match
-    the reference base. The number of bases in softClippedBasesRight is exactly equal
-    to  queryLength - queryAlignedLength - queryPosition.
-    */
-    optional string softClippedBasesRight = 31;
-
-    /*
-    Quality scores for bases in softClippedBasesLeft.  Stored in Phred Units.
-    */
-    optional bytes softClippedQualityLeft = 32;
-   /*
-    Quality scores for bases in softClippedBasesRight.  Stored in Phred Units.
-    */
-    optional bytes softClippedQualityRight = 33;
-    /*
-     Sequence for a read placed near this entry, but unmapped to the reference sequence. For instance, used to record
-     the sequence of a mate that did not map to the reference. We know that the mate maps in the proximity of this entry
-     (it is placed) but are unable to map it to a specific genomic position. The sequence is always given as obtained
-     from the reads file.
-    */
-    optional string placedUnmappedSequence=40;
-    /*
-    Quality scores for a read placed near this entry.  Phred units.
-    */
-    optional bytes placedUnmappedQuality=41;
-
-    /*
-    Read name. In SAM/BAM this is referred to as QNAME. Paired and segmented reads will have the same Read name.
-    */
-    optional string readName=42;
-}
-
-/* A link to another alignment entry. This message type is used to represent relations
-   between alignments, such as the relation between the two read fragments in a paired-end protocol,
-   or the relation between parts of reads that align through an exon exon junction and map in
-   different locations of the genome.
-  */
-message RelatedAlignmentEntry {
-    /* Target index of the location where the other alignment entry is mapped.
-      This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 target_index = 1;
-
-    /* Position on the reference where the other alignment entry is mapped. *
-       This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 position = 2;
-
-    /* Index of the fragment for the related alignment entry. This index
-       makes it possible to identify which of the read fragments mapped to the given
-       location is related to the source alignment entry.
-       This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 fragment_index = 3;
-
-    optional uint32 optimized_index=50;
-}
-
-/*
-   Represents sequence variations between the query and the reference sequences. Many variations can be represented.
-   For instance, an insertion at position 5 in the reference would be represented as from="A", to="" position=5.
-   A mutation T->G at position 6 would be rendered as from="T", to="G" position=6. Padded alignments (see SAM description)
-   can be described by a combination of pair-wise alignments, where the gap character '-' is used to indicate that no
-   base exists in the sequence considered for the alignment position, for instance:
-
-   - Padding example:
-
-    123 (<-positions)
-ref A-C
-    A-T [from="-" to=""  position=2] [from="C" to="T"  position=3]
-    ACT [from=""  to="C" position=2] [from="C" to="T"  position=3]
-    A-T [from="-" to=""  position=2] [from="C" to="T"  position=3]
-
-   - Mutation example:
-    123 (<-positions)
-ref ATT
-    ACT [from="T"  to="C" position=2]
-
-    -- Example of deletion in a read:
-    123 (<-positions)
-ref ATT
-    A-T [from="T"  to="-" position=2]
-
-    -- Example of insertion of two base pairs in a read:
-    12345 (<-positions)
-ref A--TT
-    ACCTT [from=""  to="CC" position=2]
-
-  */
-message SequenceVariation {
-    /* The reference bases. Can include one or more gap characters '-', to indicate that the reference sequence has
-     no base at this alignment position.
-     This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional string from = 2;
-    /* The read bases that differ from the reference sequence.  Can include one or more gap characters '-', to indicate
-     that the query sequence has no base at this alignment position.
-     This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional string to = 1;
-    /*
-    The position of the variation on the read, as if the read always matched on the forward strand.
-    Adding position to the index where the reference starts aligning the read yields the position of the variation
-    in reference/target sequence space. Since position starts at one the resulting position will also be one based.
-    This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 position = 3;
-    /*
-    The position of the variation, starting from the beginning of the aligned read (position 1), and up to the length
-    of the read (inclusive). Use this index if you need to know  how far the variation is observed from the beginning
-    of the sequenced read. When the read has an insertion, this index records the position immediately before the base
-    where the bases are inserted (these bases are in the to field).
-    When the read has a deletion, read_index records the position in the read after which the bases that would align
-    in the reference are missing (these bases are in the from field).
-    This field is required (enforced by semantic validation in Goby 2.0+).
-    */
-    optional uint32 read_index = 5;
-
-    /**
-      The read base quality scores for those bases that are given in the to field. This field
-      is populated when the reads used to perform the search include quality scores, and when
-      the alignment parser can extract the information from the aligner's output.
-      (this option is currently not implemented in Goby.)
-    */
-    optional bytes to_quality = 4;
-
-}
-/*
-  This message is written to 'basename'.header
-*/
-
-message AlignmentHeader {
-    /*
-     The smallest possible query index in this alignment. Data stored as an array where
-     queryIndex is the array index will be stored with only the elements in the inclusive
-     range [smallestSplitQueryIndex largestSplitQueryIndex]
-     Such data structures include queryLength and some arrays in the TooManyHits data
-     structure.
-    */
-    optional uint32 smallest_split_query_index = 9;
-    /*
-     The largest possible query index in this alignment. Data stored as an array where
-     queryIndex is the array index will be stored with only the elements in the inclusive
-     range [smallestSplitQueryIndex largestSplitQueryIndex]
-     Such data structures include queryLength and some arrays in the TooManyHits data
-     structure.
-    */
-    optional uint32 largest_split_query_index = 11;
-
-    /* Mapping from query identifier name to query index (as used in alignment entries).
-    */
-    optional IdentifierMapping query_name_mapping = 1;
-
-    /* Mapping from target identifier name to target index (as used in alignment entries).
-    */
-    optional IdentifierMapping target_name_mapping = 2;
-
-    /*
-     The number of query sequences
-    */
-    optional uint32 number_of_queries = 5;
-    /*
-      The number of target sequences
-    */
-    optional uint32 number_of_targets = 6;
-    /*
-      The number of reads that were aligned to the reference and are represented in this alignment archive.
-    */
-    optional uint32 number_of_aligned_reads = 7;
-
-    /*
-      Length of the query sequences. One number per query, in the order of increasing query index.
-      This information has been moved to the individual alignment entries.
-    */
-    repeated uint32 query_length = 3 [deprecated = true];
-    /*
-       If query length is constant across all the queries, this field contains the constant length.
-       In such cases, query_length will be empty.
-    */
-    optional uint32 constant_query_length = 10;
-
-    /*
-      Length of the target sequences. One number per target, in the order of increasing target index.
-      The target indexes must be 0..(number of targets - 1).
-    */
-    repeated uint32 target_length = 8;
-    /*
-       Indicates whether this alignment is sorted by position. True: the alignment entries occur in sorted
-       order, such that entry a occurs before entry b if a.targetIndex< b.targetIndex or, when entries
-       have the same target, when a.position < b.position.
-    */
-    optional bool sorted = 13;
-
-    /*
-       Indicates whether this alignment is indexed by position. When this attribute is true, a file called
-      'basename'.index exists that contains the AlignmentIndex message (GZip compressed).
-    */
-    optional bool indexed = 14;
-    /*
-      True when query lengths are stored in alignment entries (Goby 1.7+).
-    */
-    optional bool query_lengths_stored_in_entries = 15;
-    /*
-      Name of the aligner that produced this alignment.
-    */
-    optional string aligner_name = 17;
-    /*
-      Version number for the aligner implementation that produced this alignment.
-    */
-    optional string aligner_version = 18;
-    /*
-       The version of Goby that created this alignment file.
-    */
-    optional string version = 25;
-
-    /*
-      Sample basenames, in the order of increasing sampleIndex, starting with sampleIndex=0.
-    */
-
-    repeated string sample_basename = 30;
-
-    /*
-       This field is true when the query indices of alignment entries were permuted to smaller indices. Only sorted
-       alignments can have query_indices_were_permuted=true. When the field is true, and you need to retrieve the
-       original query-index of an alignment (because you want to retrieve the specific read(s) from a read file for
-       instance), you will need the information in the permutation file (extension basename.perm) and transform back
-       each small index of interest to the original query index.
-    */
-    optional bool query_indices_were_permuted = 26;
-    /*
-       This field is true when entries in the alignment .entries file all have the query_index_occurrences field populated
-       (Since Goby 2.0).
-    */
-    optional bool query_index_occurrences = 35;
-
-    /*
-       This field is true when entries in the alignment .entries file all have the ambiguity field populated
-       (Since Goby 2.0).
-    */
-    optional bool ambiguity_stored_in_entries = 36;
-    /*
-       This field is true when entries in the alignment .entries file all have the read_quality_score field populated.
-       (Since Goby 2.0).
-    */
-    optional bool all_read_quality_scores = 40;
-    /*
-      A description of the origin of sets of reads. Serves a similar function to BAM read groups, but more flexible and
-      efficient. Instead of storing strings, we use integers in the entries.
-      Alignemnt entries will link to a specific ReadOriginInfo with the origin_index field.
-      (Since Goby 2.0).
-    */
-    repeated ReadOriginInfo read_origin = 27;
-}
-
-message IdentifierMapping {
-    repeated IdentifierInfo mappings = 1;
-}
-
-message IdentifierInfo {
-    required string name = 1;
-    required uint32 index = 2;
-}
-
-
-/*
-     A description of the origin of sets of reads. Stored in the Goby alignment header and linked
-     from alignment entries. Goby makes it possible to adapt origin equivalence rules on the fly
-     efficiently. To do this, it is sufficient to read the header of the alignment, decide which
-     ReadOriginInfo instances are equivalent (e.g., by looking at sample, platform, library, or
-     other fields in the message), then construct a function e(a):int. This function takes
-     one originIndex parameter and returns another integer that maps to an equivalent class. The
-     equivalence class can be used to estimate error models for entries that belong to each class,
-     for instance.
-     (Since Goby 2.0).
- */
-message ReadOriginInfo {
-    /*
-       Origin index. An integer that links alignment entries to their origin information.
-    */
-    required uint32 origin_index = 1;
-    /*
-       Identifier that describes the origin of the reads. This field is compatible with the ID/platform field of BAM read
-       groups. Free text.
-    */
-    required string origin_id = 2;
-    /*
-       The sample from which the reads were sequenced. This field is compatible with the SM/sample field of BAM read
-       groups. Free text.
-    */
-    optional string sample = 4;
-    /*
-       The platform on which the reads were sequenced. This field is compatible with the PL/platform field of BAM read
-       groups. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.
-    */
-    optional string platform = 5;
-    /*
-       The library from which the reads were sequenced. This field is compatible with the LB/library field of BAM read
-       groups. Free text.
-    */
-    optional string library = 8;
-    /*
-       The platform unit on which the reads were sequenced. This field for compatibility with samtools.
-    */
-    optional string platform_unit = 12;
-    /*
-       The date the reads were sequenced. Useful to identify batch effects, in the format dd:MMM:yyyy.
-       The month is Jan, Feb, etc. to avoid all confusion with days when day<=12.
-    */
-    optional string run_date = 6;
-}
-
-/*
-  This message is written to 'basename'.tmh
-*/
-
-message AlignmentTooManyHits {
-    /*
-    The threshold used by the aligner to determine that a query is ambiguous and should be dropped.
-    Referred to as parameter k below.
-    */
-    required uint32 aligner_threshold = 2;
-    /*
-     The hits that are assigned to several (>k) reference location.
-    */
-    repeated AmbiguousLocation hits = 1;
-
-}
-
-message AmbiguousLocation {
-    /*
-     The index of the query that matched too many times.
-    */
-    required uint32 query_index = 1;
-    /*
-     The number of hits that triggered membership in the too many hits list. The query may hit more
-     locations than reported here, since some alignment tools will just drop queries that match above
-     a threshold and stop counting. This number can be >=k.
-    */
-    required uint32 at_least_number_of_hits = 2;
-    /**
-The length of the part of the query sequence that could be matched to the target (also called depth).
-May be less than the length of the query sequence, in which case the match was not perfect. When merging
-alignments produced by searching different reference sequences, consider only at_least_number_of_hits
-from alignments that have exactly the longer depth for the query. */
-    optional uint32 length_of_match = 3;
-}
-
-/*
-      This message is written to 'basename'.index
-  */
-message AlignmentIndex {
-    /*
-      Stores one element by target sequence. Each element is the cumulative target length for the target
-      stored at index i. Assume there are four target sequences, with lengths {10, 12, 15, 34}. The field
-      targetPositionOffsets will contain: {0,10,22,37}. Such offsets can be used to calculate the absolute
-      position of a genomic location. Given targetIndex and positionOnReference, the absolute location
-      is defined as  targetPositionOffsets[targetIndex]+positionOnReference.
-    */
-    repeated uint32 target_position_offsets = 1 [packed = true];
-    /*
-     The byte offsets into the compressed entries file. Byte offsets are matched with absolute position
-     by index. There should be as many elements in offsets as there are in absolutePosition
-     where chunks start which represent entries whose absolute positions are less than
-    */
-    repeated uint64 offsets = 2 [packed = true];
-    /*
-      The absolute positions of the first entry in the chunk that immediately start at offset. One element
-      per chunk in the 'basename'.entries file.
-    */
-    repeated uint64 absolute_positions = 3 [packed = true];
-
-}
diff --git a/sci-biology/goby-cpp/files/Reads.proto b/sci-biology/goby-cpp/files/Reads.proto
deleted file mode 100644
index 32c1244a3eb3..000000000000
--- a/sci-biology/goby-cpp/files/Reads.proto
+++ /dev/null
@@ -1,96 +0,0 @@
-package goby;
-
-option java_package = "edu.cornell.med.icb.goby.reads";
-option optimize_for = SPEED;
-
-message ReadCollection {
-     repeated ReadEntry reads = 1;
-}
-
-message ReadEntry {
-  /*
-    Index of a read.
-  */
-  required uint32 read_index = 1;
-   /*
-    Index of the barcode, if any.
-  */
-  optional uint32 barcode_index = 10;
-  /*
-     Read identifier/name may be present.
-  */
-  optional string read_identifier = 23;
-  /*
-     Additional description about the read (from Fasta/Q format).
-   */
-  optional string description = 22;
-  /*
-    Length of the sequence.
-   */
-  required uint32 read_length = 2;
-  /*
-    Sequence, encoded as ascii characters stored in single bytes.
-   */
-  optional bytes sequence = 3;
-  /*
-   The second sequence in a pair. Stored the same way as the sequence attribute.
-  */
-  optional bytes sequence_pair = 5;
-  /*
-    Length of the second sequence in a pair.
-  */
-  optional uint32 read_length_pair = 6;
-  /*
-    Quality scores in Phred units, stored as single bytes (0-255).
-  */
-  optional bytes quality_scores = 4;
-  /*
-    Quality scores for the second sequence in a pair. Stored as the 'qualityScores' attribute.
-   */
-  optional bytes quality_scores_pair = 7;
-  /*
-    Compressed stream of data. The first byte indicates the compression/decompression method (codec). The remaining bytes are
-    content compressed with the codec.
-  */
-  optional bytes compressed_data = 8;
-  /*
-     Stores meta-data about the reads. Typically meta-data is stored in the very first read of a
-     read collection, with the understanding that the meta-data applies to all the reads in the
-     collection. Meta-data can be used to store information about when the sample was sequenced,
-     or other information of interest. The key-value pair format is sufficiently flexible to
-     accomodate a variety of needs. The following keys are pre-defined. Please use pre-defined
-     keys so that automated tools can use metadata in relatively standard way. Please note that
-     some keys provide a format for the value. This format should also be followed to garantee
-     that meta data can be used computationally in fully automatic manner.
-
-     key="sequencing-run-start-date" value="MM/DD/YYYY" Used to record when the sequencing run
-     was initiated on the instrument. Can be used to detect batch effect in a large set of samples.
-     key="platform" value="<free-text>". Value is free text, but the following terms are pre-defined.
-      Illumina GaIIx
-      Illumina HiSeq 1000
-      Illumina HiSeq 2000
-      Helicos Heliscope
-      LifeTech 5500 SOLiD
-      LifeTech 5500xl SOLiD
-      Roche 454 GS FLX Ti
-
-      key="organism" value="species name"
-      Since Goby 1.9.1
-  */
-  repeated MetaData meta_data = 25;
-
-}
-/*
- A message to store a key/value pair and represent metadata about reads.
- Since Goby 1.9.1
- */
-message MetaData {
- /*
-   Provides the key. See examples in the documentation of meta_data for ReadEntry.
- */
- required string key=1;
- /*
-   Describes the value associated with the key. See examples in the documentation of meta_data for ReadEntry.
- */
- required string value=2;
-}
diff --git a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch b/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch
deleted file mode 100644
index 415785466af7..000000000000
--- a/sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index 1033382..33ca906 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -84,7 +84,7 @@ GobyReadsStats_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_D
- GobyReadsStats_SOURCES = \
- 	GobyReadsStats.cc
- 
--GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
-+GobyFastaToCompact_LDADD = libgoby.la ${BOOST_LDFLAGS} ${BOOST_SYSTEM_LIB} ${BOOST_DATE_TIME_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} -lz
- GobyFastaToCompact_SOURCES = \
- 	GobyFastaToCompact.cc
- 
diff --git a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
index fcf8971fceb0..e74dd6ecede3 100644
--- a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
+++ b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -9,7 +9,8 @@ inherit autotools-utils
 
 DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
 HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip
+	https://dev.gentoo.org/~mgorny/dist/${P}-files.tar.bz2"
 
 LICENSE="GPL-3"
 SLOT="0"
@@ -24,7 +25,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/${PV}/cpp"
 
 PATCHES=(
-	"${FILESDIR}"/${P}-underlinking.patch
+	"${WORKDIR}"/${P}-files/${P}-underlinking.patch
 )
 
 src_prepare() {
@@ -33,7 +34,7 @@ src_prepare() {
 		-i src/Makefile.am || die
 
 	pushd src/goby > /dev/null || die
-	cp "${FILESDIR}"/*.proto . || die
+	cp "${WORKDIR}"/${P}-files/*.proto . || die
 	protoc --cpp_out=. *.proto || die
 	popd > /dev/null || die