alignment.md

Manta Developer Guide - Alignment Library

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Table of Contents

• Introduction
• Debugging
• Running single alignment unit tests

Introduction

This is a subsection of the manta developer guide focusing on the alignment library.

Debugging

All alignment methods support debugging via the DEBUG_ALN symbol. When defined, the score matrix and backtrace pointer for each element in the alignment structure are streamed to stderr, in addition to the backtrace sequence. Due to the volume of output, this can be most usefully applied to a single, relatively small alignment unit test.

For even richer debugging DEBUG_ALN_MATRIX can be defined. In this case the entire score matrix is saved (this is normally discarded as soon as each element row is no longer required), and the score+backpointer matrix for each state is printed to stderr. This is only effective for very small unit test cases.

Running single alignment unit tests

Note that unit tests can be run outside of the manta build system, and additionally reduced to run a single test suite or single test. This can be usefully combined with the rich debug output options above. Note that this test selection interface is a standard defined by the boost unit test library.

To run unit tests directly. First go through the standard build procedure. Then from the build directory, the alignment unit tests can be run by executing:

src/c++/lib/alignment/test/manta_unit_test_alignment

You can run the tests for the, e.g. intron aligner only using the -t option as follows:

src/c++/lib/alignment/test/manta_unit_test_alignment -t test_GlobalJumpIntronAligner

...or select as single test out of this test suite:

src/c++/lib/alignment/test/manta_unit_test_alignment -t test_GlobalJumpIntronAligner/test_GlobalJumpAlignerSplice