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samtools sort -m 5000000 unsorted_in.bam sorted_out Read the specified unsorted_in.bam as input, sort it in blocks up to 5 million k (5 Gb) [ units verification needed ] and write output to a series of bam files named sorted_out.0000.bam , sorted_out.0001.bam , etc., where all bam 0 reads come before any bam 1 read, etc. [ verification needed ]
Binary Alignment Map (BAM) is the comprehensive raw data of genome sequencing; [1] it consists of the lossless, compressed binary representation of the Sequence Alignment Map-files. [2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4]
The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present.
www.htslib.org /doc /samtools-mpileup.html Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment.
Edit-tricks are most useful when multiple tables must be changed, then the time needed to develop complex edit-patterns can be applied to each table. For each table, insert an alpha-prefix on each column (making each row-token "|-" to sort as column zero, like prefix "Row124col00"), then sort into a new file, and then de-prefix the column entries.
In the tables below, all columns sort correctly. The wikitext for the first entry in each table in the first row is shown in the table header. Note: None of the table columns use the data-sort-type= modifier. Using data-sort-type= can sometimes break sorting when used with the template.
Indexes can be created using one or more columns of a database table, providing the basis for both rapid random lookups and efficient access of ordered records. An index is a copy of selected columns of data, from a table, that is designed to enable very efficient search. An index normally includes a "key" or direct link to the original row of ...
To use column-major order in a row-major environment, or vice versa, for whatever reason, one workaround is to assign non-conventional roles to the indexes (using the first index for the column and the second index for the row), and another is to bypass language syntax by explicitly computing positions in a one-dimensional array.