[BARNA-273] Implement stranded annotation mapping for BAM input files - Jira

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Type: Bug
Status: Resolved
Priority: Blocker
Resolution: Fixed
Affects Version/s: AStalavista 3.1 (API 1.21)
Fix Version/s: Capacitor 1.2.4 (API 1.22), Capacitor 1.3 (API 1.23)
Component/s: Capacitor
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Description

In the SAM format we have no sense/antisense information on the reads.

We can implement stranded annotation mapping using additional information provided by the user.

Implement the following new parameter structure to better define the information:

READ_DESCRIPTOR -> [NONE, // default 
                    SIMPLE,
                    PAIRED,
                    STRANDED
                   ]

READ_STRAND -> [NONE, // default
                SENSE,
                ASENSE,
                MATE1_SENSE,
                MATE2_SENSE
               ]


ANNOTATION_MAPPING -> [AUTO, // default, maximum information
                       SINGLE, 
                       PAIRED, 
                       SINGLE_STRANDED,
                       PAIR_STRANDED                       
                      ]

BAM files with mixed single/paired/stranded/unstranded reads are not supported so far.

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Assignee:: Emilio Palumbo

Reporter:: Emilio Palumbo

Votes:: 0 Vote for this issue

Watchers:: 3 Start watching this issue

Dates

Created:: 27/Nov/12 3:49 PM

Updated:: 09/Oct/15 4:20 AM

Resolved:: 12/Nov/13 9:54 AM