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459 bytes added
, 16:01, 14 November 2012
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| Returns the SamStatus for the reads/writes. 0 on success. | | Returns the SamStatus for the reads/writes. 0 on success. |
| | | |
− | = Example Output = | + | = Examples = |
| | | |
− | If the number to trim from each side is the same:
| + | ==Trim the same number of bases from each side== |
| + | Example Input, trimming 2 bases: |
| + | <pre> |
| + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam 2 |
| + | </pre> |
| + | Example Output: |
| <pre> | | <pre> |
| Arguments in effect: | | Arguments in effect: |
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| </pre> | | </pre> |
| | | |
− | If the number to trim from each side is different (but left/right is the same for forward/reverse):
| + | ==Trim different bases from each side, but treat forward & reverse the same== |
| + | Example Input, trimming 1 base from the left and 2 bases from the right: |
| + | <pre> |
| + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 |
| + | </pre> |
| + | Example Output: |
| <pre> | | <pre> |
| Arguments in effect: | | Arguments in effect: |
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| | | |
− | If the number to trim from each side is different and the reverse option is used(left/right is opposite for reverse):
| + | ==Trim different bases from each side, but treat reverse strands the opposite== |
| + | Example Input, trimming 1 base from the left and 2 bases from the right for forward strands and do the opposite for reverse strands: |
| + | <pre> |
| + | ./bin trimBam testFiles/testSam.sam results/trimSam.sam -L 1 -R 2 --reverse |
| + | </pre> |
| + | Example Output: |
| <pre> | | <pre> |
| Arguments in effect: | | Arguments in effect: |