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sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.

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Exiting from the software immediately after visiting unmapped reads

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The software is working very good, except the case when an unmapped read is in the middle of SAM file. Then it exits the software with this message **shift_cigar failed....

mahdiheydari avatar mahdiheydari

program hanging

Hi, could you help me understand why this program hangs on this file and cannot process it (it's a 3 line sam file). Thanks [1.txt](https://github.com/mlafave/sam2pairwise/files/1475512/1.txt)

abayega avatar abayega

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verified publisher icon mlafave

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sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.

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