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Old 06-10-2009, 11:37 AM   #1
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116
Default MAQ demands pairs have the same length?

I'm using 0.7.1

I consistently get one of the two errors when running "maq match" when pairs have different sequence lengths (due to trimming)

maq: read.cc:61: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strncmp(name, lr->name[j], tl-1) == 0' failed.

maq: read.cc:58: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `l >= size_r' failed.
Aborted

I am forced to set the -1 and -2 options to the shortest sequence in the run. This seems too restrictive to me. What is the logic behind this and why are there separate -1 and -2 options if they have to be set to the same length anyway?
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Old 06-10-2009, 01:03 PM   #2
Zigster
(Jeremy Leipzig)
 
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i suspect MAQ might be even more restrictive than I first assumed

it appears read length cannot vary at all

is this true?
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Old 06-10-2009, 03:30 PM   #3
Zigster
(Jeremy Leipzig)
 
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i guess so
Quote:
# Is Maq able to deal with reads with variable lengths?

No and yes. In alignment, all the reads must be in the same length. However, you can `mapmerge' several alignments from reads in different lengths and after that all the subsequent maq commands accept variable lengths.
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Old 06-11-2009, 01:52 AM   #4
dvh
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novoalign will do variable read lengths, and has all maq functionality.
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