The number of pairwise alignments recorded in a CodaChrome matrix file often exceeds the number of pixels on a typical computer monitor.
For each pair of reads, the aligner produces a pair of alignment records.
BamView uses and is distributed with the Java library Picard (http://picard.sourceforge.net) to retrieve read alignment records from data files in BAM format.
The latter is challenging because, in the SAM format, an alignment of a read pair is described by a pair of alignment records, which cannot be expected to be adjacent to each other.
The alignment records and the target array make up a single data structure with the batch of reads, which is passed to the next stage once all the reads in the batch have been processed through the BWT queue (which contains both mapped and unmapped reads).
If another exact seed with smaller offset exists in the read the alignment is filtered as a duplicate, otherwise the alignment is recorded.
This check was done with Perl scripts (available upon request) applying the following procedure: first, the maximal alignment length of a given multiple amino acid sequence alignment was recorded.
Genome sequencing data on scaffold87443 from 10 sequenced cultivars were aligned; all SNP markers and InDel markers from the sequence alignment were recorded (Additional file 3).
All preoperative and postoperative HHS and WOMAC scores, as well as blood loss, surgical time, hospital stay and radiographic stem alignment were recorded in a standard Excel file (Microsoft Office, Microsoft Corporation, Seattle, WA) and compared between groups.
Pre- and postoperative leg alignment was recorded on long leg radiographs.
