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authorMichał Górny <mgorny@gentoo.org>2017-12-10 00:20:58 +0100
committerMichał Górny <mgorny@gentoo.org>2017-12-10 01:05:28 +0100
commit9410f41fefdcd2fb758ae0b6921fb66be1d98378 (patch)
tree351524b24742e673d7f6f326c89cb7e4265775b9 /sci-biology
parentgames-action/*: Update Manifest hashes (diff)
downloadgentoo-9410f41fefdcd2fb758ae0b6921fb66be1d98378.tar.gz
gentoo-9410f41fefdcd2fb758ae0b6921fb66be1d98378.tar.bz2
gentoo-9410f41fefdcd2fb758ae0b6921fb66be1d98378.zip
sci-biology/goby-cpp: [QA] Move aux files to a distfile
Closes: https://bugs.gentoo.org/620614
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/goby-cpp/Manifest7
-rw-r--r--sci-biology/goby-cpp/files/Alignments.proto597
-rw-r--r--sci-biology/goby-cpp/files/Reads.proto96
-rw-r--r--sci-biology/goby-cpp/files/goby-cpp-2.0.1-underlinking.patch16
-rw-r--r--sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild9
5 files changed, 9 insertions, 716 deletions
diff --git a/sci-biology/goby-cpp/Manifest b/sci-biology/goby-cpp/Manifest
index 88622e3c813..2bd240a998a 100644
--- a/sci-biology/goby-cpp/Manifest
+++ b/sci-biology/goby-cpp/Manifest
@@ -1,3 +1,4 @@
-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
+DIST goby_1.9.8.1-cpp.zip 134904 BLAKE2B 800f3bcbe9f721bfb636f514630fb1ceba3a1fe41616f63fc15f9f2a24394ef9be90419ccad0c9bd8b29100eeaea57659ba013042cf4a11b6038fc6dee782619 SHA512 d31cd7f0be19074bfe8da74d9f2510f0e0f15fe6c485bbed8520052468d2cd2f1bc5fcad8b0d6a1586f5acde73db326059f45994ecfbb5fb6c09692d8e155190
+DIST goby_2.0.1-cpp.zip 177718 BLAKE2B 666b50fdc199693f8a4f9b6007f6609e91ab6093b643da88e580c9a3438a150cd7be78d2b5dcdd2fe905263d32ebbac1e0e47dbc637fd5d59f877e7cbdaaeeb2 SHA512 992bd10d5538dec1478820f26151dd311f4de13e7947b49f0b06d6cbdd4b71deeb3aa8a4c6a598fb92fbcb9cbf4ff97bf81205c9389d4a0da4443317e48aea9f
diff --git a/sci-biology/goby-cpp/files/Alignments.proto b/sci-biology/goby-cpp/files/Alignments.proto
deleted file mode 100644
index fe7f5664764..00000000000
--- 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 32c1244a3eb..00000000000
--- 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 415785466af..00000000000
--- 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} ${BOOST_PROGRAM_OPTIONS_LIB} -lz
- GobyFastaToCompact_SOURCES = \
- GobyFastaToCompact.cc
-
diff --git a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
index fcf8971fceb..e74dd6ecede 100644
--- a/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
+++ b/sci-biology/goby-cpp/goby-cpp-2.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -9,7 +9,8 @@ inherit autotools-utils
DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
HOMEPAGE="http://campagnelab.org/software/goby/"
-SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${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