New upstream version 2.1.1+dfsg

CXXFLAGS += -O3 -std=c++11 -Isrc -I@capnp@/include -I@mathinc@

CXXFLAGS += -O3 -std=c++14 -Isrc -I@capnp@/include -I@mathinc@

CPPFLAGS += @amcppflags@

UNAME_S=$(shell uname -s)

	AC_MSG_ERROR([Cap'n Proto compiler (capnp) not found.])

fi

CPPFLAGS="-I$with_capnp/include -std=c++11"

CPPFLAGS="-I$with_capnp/include -std=c++14"

AC_CHECK_HEADER(capnp/common.h, [result=1], [result=0])

`SRR2671867.BaAmes.poretools.fastq.gz <http://gembox.cbcb.umd.edu/mash/SRR2671867.BaAmes.poretools.fastq.gz>`_: Nanopore 1D + 2D sequences generated by poretools (157MB)

`SRR2671868.Bc10987.poretools.fastq.gz <http://gembox.cbcb.umd.edu/mash/SRR2671868.Bc10987.poretools.fastq.gz>`_: Nanopore 1D + 2D sequences generated by poretools (250MB)

Mash Screen: High-throughput sequence containment estimation for genome discovery

---------------------------------------------------------------------------------

Custom scripts and intermediate data:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

`MashScreen_supp.tar.gz <https://obj.umiacs.umd.edu/mash/screen/MashScreen_supp.tar.gz>`_

Data files:

~~~~~~~~~~~

Mash Sketch databases for RefSeq release 88:

 * `RefSeq88n.msh.gz <https://obj.umiacs.umd.edu/mash/screen/RefSeq88n.msh.gz>`_: Genomes (k=21, s=1000), 1.2Gb uncompressed

 * `RefSeq88p.msh.gz <https://obj.umiacs.umd.edu/mash/screen/RefSeq88p.msh.gz>`_: Proteomes (k=9, s=1000), 1.1Gb uncompressed

`art.fastq.gz <https://obj.umiacs.umd.edu/mash/screen/art.fastq.gz>`_: Simulated reads for Shakya experiment

Figure 5:

 * `fig5.html <https://obj.umiacs.umd.edu/mash/screen/fig5/fig5.html>`_: Interactive version

 * `fig5.tsv <https://obj.umiacs.umd.edu/mash/screen/fig5/fig5.tsv>`_: Source data

Public data sources

~~~~~~~~~~~~~~~~~~~

The BLAST ``nr`` database was downloaded from ``ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*``.

HMP data were downloaded from ``ftp://public-ftp.ihmpdcc.org/``, reads from the ``Ilumina/`` directory

and coding sequences from the ``HMGI/`` directory. Within these folders, sample SRS015937 resides in

``tongue_dorsum/`` and SRS020263 in ``right_retroauricular_crease/``.

SRA runs downloaded with the `SRA Toolkit <https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/>`_.

RefSeq genomes downloaded from the ``genomes/refseq/`` directory of ``ftp.ncbi.nlm.nih.gov``.

Public data products

~~~~~~~~~~~~~~~~~~~~

Quebec Polyomavirus is submitted to GenBank as BK010702.

Screen of SRA metagenomes vs. RefSeq

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * `sra_meta_nucl_95idy.tsv.gz <https://obj.umiacs.umd.edu/mash/screen/tables/sra_meta_nucl_95idy.tsv.gz>`_ (2.3Gb uncompressed)

 * `sra_meta_nucl_80idy_3x.tsv.gz <https://obj.umiacs.umd.edu/mash/screen/tables/sra_meta_nucl_80idy_3x.tsv.gz>`_ (6.7Gb uncompressed)

 * `sra_meta_prot_95idy.tsv.gz <https://obj.umiacs.umd.edu/mash/screen/tables/sra_meta_prot_95idy.tsv.gz>`_ (2.1Gb uncompressed)

 * `sra_meta_prot_80idy_3x.tsv.gz <https://obj.umiacs.umd.edu/mash/screen/tables/sra_meta_prot_80idy_3x.tsv.gz>`_ (8.3Gb uncompressed)

These files have a line for each RefSeq genome listing all metagenomic SRA runs

(as of August 2018) with Mash Containment Scores above the specified threshold.

They are provided for two screen modes:

* ``nucl``: Genomic RefSeq sequences

* ``prot``: Proteomic RefSeq sequences (combined amino acid sequences per organism). **NOTE:** Protein tables above are not p-value filtered and thus large (> ~50Gb) runs may have spurious hits. They also do not contain plasmids. Updates coming soon!

...and at two thresholds:

* ``95idy``: 95% Mash Containment Score, any coverage. Useful for finding runs containing a specific genome.

* ``80idy_3x``: 80% Mash Containment Score, at least 3x median k-mer multiplicity.

  Useful for finding related, but novel, sequences.

The files are tab separated, with each line beginning with a RefSeq assembly accession, followed by SRA accessions, for example:

::

  GCF_000001215.4	SRR3401361	SRR3540373

  GCF_000001405.36	SRR5127794	ERR1539652	SRR413753	ERR206081

  GCF_000001405.38	SRR5127794	ERR1539652	ERR1711677	SRR413753	ERR206081

	for ( unordered_set<MinHashHeap *>::const_iterator i = minHashHeaps.begin(); i != minHashHeaps.end(); i++ )

	{

		HashList hashList(parameters.kmerSize);

		HashList hashList(parameters.use64);

		(*i)->toHashList(hashList);

				break;

			}

			//kmersTotal++; TODO

			if ( ! noncanonical )

			{

				bool debug = false;

				useRevComp = true;

				bool prefixEqual = true;

				if ( debug ) {for ( uint64_t k = j; k < j + kmerSize; k++ ) { cout << *(seq + k); } cout << endl;}

				for ( uint64_t k = 0; k < kmerSize; k++ )

				{

					char base = seq[j + k];

					char baseMinus = seqRev[l - j - kmerSize + k];

					if ( debug ) cout << baseMinus;

					if ( prefixEqual && baseMinus > base )

					{

						useRevComp = false;

						break;

					}

					if ( prefixEqual && baseMinus < base )

					{

						prefixEqual = false;

					}

				}

				if ( debug ) cout << endl;

			}

			const char * kmer;

			if ( trans )

			}

			else

			{

				kmer = useRevComp ? seqRev + l - j - kmerSize : seq + j;

				const char *kmer_fwd = seq + j;

				const char *kmer_rev = seqRev + length - j - kmerSize;

				kmer = (noncanonical || memcmp(kmer_fwd, kmer_rev, kmerSize) <= 0) ? kmer_fwd : kmer_rev;

			}

			//cout << kmer << '\t' << kmerSize << endl;

			hash_u hash = getHash(kmer, kmerSize, seed, use64);

			//cout << kmer << '\t' << hash.hash64 << endl;

			input->minHashHeap->tryInsert(hash);

			uint64_t key = use64 ? hash.hash64 : hash.hash32;

			if ( input->hashCounts.count(key) == 1 )

    addOption("list", Option(Option::Boolean, "l", "Input", "List input. Lines in each <input> specify paths to sequence files, one per line.", ""));

    addOption("prefix", Option(Option::File, "o", "Output", "Output prefix (first input file used if unspecified). The suffix '.msh' will be appended.", ""));

    addOption("id", Option(Option::File, "I", "Sketch", "ID field for sketch of reads (instead of first sequence ID).", ""));

    addOption("comment", Option(Option::File, "C", "Sketch", "Comment for a sketch of reads (instead of first sequence comment.", ""));

    addOption("comment", Option(Option::File, "C", "Sketch", "Comment for a sketch of reads (instead of first sequence comment).", ""));

    useSketchOptions();

}