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The code needs to figure out the strand and reverse compliment the reverse strands.
The code needs to figure out the strand and reverse compliment the reverse strands.
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One file for the first in pair & 1 file for the 2nd in the pair - the order in the two files must match.
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Reverse complimenting means:
Reverse complimenting means:
** It would also error if the read is not paired.
** It would also error if the read is not paired.
*Later Release: work on unsorted BAM files.
*Later Release: work on unsorted BAM files.
** Prefer to sort at the same time as writing the FASTQ files rather than 1 step to sort and a 2nd step to write the FASTQs.
** Would be useful to have something implemented within the library (would be useful for dedupping, etc, but might be tricky to implement as API - sometimes the pair may be far apart.
*** maybe something like SamFile::getNextReadPair or SamFileHelper::getNextReadPair due to bookkeeping, may be useful to separate it out from the SamFile - either would return handle the logic and return a pair of records
*** At some point may have to start writing a file.
*** could attempt to just store the readname and FilePosition and use random access to jump around when a pair is found (but that would be inefficient if they are close) - and it would depend on how big the file is to whether or not readname & filePosition would still be storing too much information
*** A two scan approach on the original BAM may be the best
*Separate suggestion: implement is a smart pileup - which retains a clone of SamRecord until you see the mate pair
** useful in the dedupper and variant caller and etc but we probably need to discuss if we decide to implement it
=== Proposed Solution ===
=== Proposed Solution ===
